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1.  The DNA Translocase FANCM/MHF Promotes Replication Traverse of DNA Interstrand Crosslinks 
Molecular cell  2013;52(3):10.1016/j.molcel.2013.09.021.
SUMMARY
The replicative machinery encounters many impediments, some of which can be overcome by lesion bypass or replication restart pathways, leaving repair for a later time. However, interstrand crosslinks (ICLs), which preclude DNA unwinding, are considered absolute blocks to replication. Current models suggest that fork collisions, either from one or both sides of an ICL, initiate repair processes required for resumption of replication. To test these proposals, we developed a single molecule technique for visualizing encounters of replication forks with ICLs, as they occur in living cells. Surprisingly, the most frequent patterns were consistent with replication traverse of an ICL, without lesion repair. The traverse frequency was strongly reduced by inactivation of the translocase and DNA binding activities of the FANCM/MHF complex. The results indicate that translocase-based mechanisms enable DNA synthesis to continue past ICLs, and that these lesions are not always absolute blocks to replication.
doi:10.1016/j.molcel.2013.09.021
PMCID: PMC3880019  PMID: 24207054
2.  Molecular cloning, overexpression, and an efficient one-step purification of α5β1 integrin 
Protein expression and purification  2013;92(1):10.1016/j.pep.2013.08.013.
The α5β1 integrin heterodimer is involved in many cellular processes and is an anticancer therapeutic target. Therefore, access to quantities of protein suitable for studies aimed at understanding its biological functions is important. To this end, a large-scale protein expression system, utilizing the recombinant baculovirus/SF9 insect cell expression system, was created to produce the extracellular domain of the α5β1 integrin. An incorporated 8X-histidine tag enabled one-step nickel-column purification. Following sequence confirmation by LC-MS/MS, the conformation of the heterodimer was characterized by native dot blot and negative stain electron microscopy. Cellular transduction inhibition studies confirmed biological activity. The system allows expression and purification of α5β1 integrin in quantities suitable for an array of different experiments including structural biology.
doi:10.1016/j.pep.2013.08.013
PMCID: PMC3873862  PMID: 23993979
α5β1 integrin expression; pFastBac1 vector; recombinant baculovirus; electron microscopy
3.  Recognition of Protein-coding Genes Based on Z-curve Algorithms 
Current Genomics  2014;15(2):95-103.
Recognition of protein-coding genes, a classical bioinformatics issue, is an absolutely needed step for annotating newly sequenced genomes. The Z-curve algorithm, as one of the most effective methods on this issue, has been successfully applied in annotating or re-annotating many genomes, including those of bacteria, archaea and viruses. Two Z-curve based ab initio gene-finding programs have been developed: ZCURVE (for bacteria and archaea) and ZCURVE_V (for viruses and phages). ZCURVE_C (for 57 bacteria) and Zfisher (for any bacterium) are web servers for re-annotation of bacterial and archaeal genomes. The above four tools can be used for genome annotation or re-annotation, either independently or combined with the other gene-finding programs. In addition to recognizing protein-coding genes and exons, Z-curve algorithms are also effective in recognizing promoters and translation start sites. Here, we summarize the applications of Z-curve algorithms in gene finding and genome annotation.
doi:10.2174/1389202915999140328162724
PMCID: PMC4009845  PMID: 24822027
Genome annotation; Genome re-annotation; Z-curve algorithm; ZCURVE; ZCURVE_V.
4.  Optimizing the transduction efficiency of human hematopoietic stem cells using capsid-modified AAV6 vectors in vitro and in a xenograft mouse model in vivo 
Cytotherapy  2013;15(8):986-998.
Background
Although recombinant adeno-associated virus serotype 2 (AAV2) vectors have gained attention owing to their safety and efficacy in number of Phase I/II clinical trials, their transduction efficiency in hematopoietic stem cells (HSCs) has been reported to be low. Only a handful of additional AAV serotype vectors have been evaluated, and comparative analyses of their transduction efficiency in HSCs from different species have not been performed.
Methods
Here, we evaluated the transduction efficiency of all available AAV serotype vectors (AAV1 through AAV10) in primary mouse, cynomolgus monkey, and human HSCs, respectively. The transduction efficiency of the optimized AAV vectors was also evaluated in human HSCs in a murine xenograft model in vivo.
Results
We observed that although there are only six amino acid differences between AAV1 and AAV6, AAV1, but not AAV6, transduce mouse HSCs cells well, whereas AAV6, but not AAV1, transduce human HSCs well. None of the 10 serotypes transduce cynomolgus monkey HSCs in vitro. We also evaluated the transduction efficiency of AAV6 vectors containing mutations in surface-exposed tyrosine residues, and observed that tyrosine (Y) to phenylalanine (F) point mutations in residues 445, 705, and 731, led to a significant increase in transgene expression in human HSCs in vitro and in a mouse xenograft model in vivo.
Discussion
These studies suggest that the tyrosine-mutant AAV6 serotype vectors are the most promising vectors for transducing human HSCs, and that it is possible to further increase the transduction efficiency of these vectors for their potential use in HSC-based gene therapy in humans.
doi:10.1016/j.jcyt.2013.04.003
PMCID: PMC3711144  PMID: 23830234
AAV vectors; hematopoietic stem cells; gene transfer; gene expression
5.  Association of napping and night-time sleep with impaired glucose regulation, insulin resistance and glycated haemoglobin in Chinese middle-aged adults with no diabetes: a cross-sectional study 
BMJ Open  2014;4(7):e004419.
Objective
To assess associations between napping and night-time sleep duration with impaired glucose regulation, insulin resistance (IR) and glycated haemoglobin (HbA1c).
Design
Cross-sectional study.
Setting
Fujian Province, China, from June 2011 to January 2012.
Participants
This study enrolled 9028 participants aged 40–65 years. Data of 7568 participants with no diabetes were included for analysis. Type 2 diabetes was defined applying WHO criteria.
Outcome measures
Participants’ daytime napping and night-time sleep duration data were collected using a standardised self-reported Chinese-language questionnaire about sleep frequency and quality. Anthropometric and laboratory parameters were also measured. IR was defined as a HOMA-IR index value >2.50. ORs and 95% CIs were derived from multivariate logistic regression models.
Results
Participants (mean age 51.1±7.0 years) included 3060 males and 4508 females with average night-time sleep of 7.9 h. A higher proportion of males napped than females. After adjustment for potential confounders, ORs for HbA1c >6.0% were 1.28 and 1.26 for those napping ≤1 h and >1 h (p=0.002 and p=0.018), respectively. Statistically significant differences in IR between nappers and non-nappers were only marginal clinically. Odds for HbA1c >6.0% were significantly lower in participants with longer night-time sleep durations than in the reference group (>8 h vs 6–8 h). Odds for IR were significantly lower in participants whose night-time sleep hours deviated from the reference group (<6 h, >8 h vs 6–8 h)
Conclusions
Chinese middle-aged adults with no diabetes who napped had higher HbA1c and IR; those with shorter night-time sleep durations had increased HbA1c. Night-time sleep hours that are either <6 or >8 tend to be associated with lower odds for IR. Further studies are necessary to determine the underlying clinical significance and mechanisms behind these associations.
doi:10.1136/bmjopen-2013-004419
PMCID: PMC4120253  PMID: 25056969
SLEEP MEDICINE
6.  Effect of Age and Biological Subtype on the Risk and Timing of Brain Metastasis in Breast Cancer Patients 
PLoS ONE  2014;9(2):e89389.
Background
Brain metastasis is a major complication of breast cancer. This study aimed to analyze the effect of age and biological subtype on the risk and timing of brain metastasis in breast cancer patients.
Patients and Methods
We identified subtypes of invasive ductal carcinoma of the breast by determining estrogen receptor, progesterone receptor and HER2 status. Time to brain metastasis according to age and cancer subtype was analyzed by Cox proportional hazard analysis.
Results
Of the 2248 eligible patients, 164 (7.3%) developed brain metastasis over a median follow-up of 54.2 months. Age 35 or younger, HER2-enriched subtype, and triple-negative breast cancer were significant risk factors of brain metastasis. Among patients aged 35 or younger, the risk of brain metastasis was independent of biological subtype (P = 0.507). Among patients aged 36–59 or >60 years, those with triple-negative or HER2-enriched subtypes had consistently increased risk of brain metastasis, as compared with those with luminal A tumors. Patients with luminal B tumors had higher risk of brain metastasis than luminal A only in patients >60 years.
Conclusions
Breast cancer subtypes are associated with differing risks of brain metastasis among different age groups. Patients age 35 or younger are particularly at risk of brain metastasis independent of biological subtype.
doi:10.1371/journal.pone.0089389
PMCID: PMC3933537  PMID: 24586742
7.  Production of shikimic acid from Escherichia coli through chemically inducible chromosomal evolution and cofactor metabolic engineering 
Background
Shikimic acid (SA) produced from the seeds of Chinese star anise (Illicium verum) is a key intermediate for the synthesis of neuraminidase inhibitors such as oseltamivir (Tamiflu®), an anti-influenza drug. However, plants cannot deliver a stable supply of SA. To avoid the resulting shortages and price fluctuations, a stable source of affordable SA is required. Although recent achievements in metabolic engineering of Escherichia coli strains have significantly increased SA productivity, commonly-used plasmid-based expression systems are prone to genetic instability and require constant selective pressure to ensure plasmid maintenance. Cofactors also play an important role in the biosynthesis of different fermentation products. In this study, we first constructed an E. coli SA production strain that carries no plasmid or antibiotic marker. We then investigated the effect of endogenous NADPH availability on SA production.
Results
The pps and csrB genes were first overexpressed by replacing their native promoter and integrating an additional copy of the genes in a double gene knockout (aroK and aroL) of E. coli. The aroG fbr , aroB, aroE and tktA gene cluster was integrated into the above E. coli chromosome by direct transformation. The gene copy number was then evolved to the desired value by triclosan induction. The resulting strain, E. coli SA110, produced 8.9-fold more SA than did the parental strain E. coli (ΔaroKΔaroL). Following qRT-PCR analysis, another copy of the tktA gene under the control of the 5Ptac promoter was inserted into the chromosome of E. coli SA110 to obtain the more productive strain E. coli SA110. Next, the NADPH availability was increased by overexpressing the pntAB or nadK genes, which further enhanced SA production. The final strain, E. coli SA116, produced 3.12 g/L of SA with a yield on glucose substrate of 0.33 mol/mol.
Conclusion
An SA-producing E. coli strain that carries neither a plasmid nor an antibiotic marker was constructed by triclosan-induced chromosomal evolution. We present the first demonstration that increasing NADPH availability by overexpressing the pntAB or nadK genes significantly enhances SA production.
doi:10.1186/1475-2859-13-21
PMCID: PMC3923554  PMID: 24512078
Shikimic acid; Escherichia coli; Chemically induced chromosomal evolution; NADPH; Transhydrogenase; NAD kinase
8.  Polyadenylated Messenger RNA in Paired Helical Filament-Immunoreactive Neurons in Alzheimer Disease 
Summary
An antibody raised against isolated paired helical filaments (PHF) was used to identify tangle-bearing (PHF+) neurons in autopsy brain tissue from six Alzheimer disease (AD) patients and six age-matched controls (AMC). A comparison of the levels of polyadenylated messenger RNA [poly(A)+ mRNA] in PHF+ and PHF− neurons of similar cross-sectional area in temporal and parietal lobe and cerebellum from four AD and four AMC brains was made by analysis of in situ hybridization of [3H] polyuridylate [poly(U)] to intracellular poly(A)+ mRNA. In PHF+ neurons, the level of poly(A)+. mRNA was approximately two-thirds that in similar-sized PHF− neurons in either AD or AMC. The level of poly(A)+ mRNA in PHF− neurons in regions of the brain that have more of the histopathologically defined effects in AD was similar to that in regions with less effects.
PMCID: PMC3886638  PMID: 1972628
Paired helical filament; Tangle-bearing neurons; Alzheimer disease; Polyadenylated messenger RNA
9.  Ursolic Acid Provides Kidney Protection in Diabetic Rats☆ 
Background
Diabetic nephropathy (DN) is one of the most serious microvascular complications of diabetes and the leading cause of end-stage renal failure. However, the treatment of DN is still a problem in the world. Inflammatory process plays a critical role in the development of DN. Therefore, anti-inflammatory treatment of DN is worth exploring now and in the future.
Objective
The study aimed to evaluate the impact of ursolic acid (UA) on renal function in streptozotocin-induced diabetes.
Methods
Rats with streptozotocin-induced diabetes were treated with UA for 16 weeks. After 16 weeks, urine albumin excretion, serum creatinine, and blood urea nitrogen were measured. In addition, renal oxidative stress level, nuclear factor kappa-B (NF-κB) activity, P-selectin expression, and kidney histopathologic changes were evaluated.
Results
Sixteen weeks following streptozotocin injection, the rats produced significant alteration in renal function and increased oxidative stress, NF-κB activity, and P-selectin expression in the kidneys. Interestingly, UA significantly prevented biochemical and histopathologic changes in the kidneys associated with diabetes. Compared with untreated diabetic rats, UA treatment lowered urine albumin excretion, renal oxidative stress level, NF-κB activity, and P-selectin expression. Moreover, UA treatment also improved renal histopathologic changes in rats with diabetes.
Conclusions
UA treatment exhibited a protective effect on kidneys in diabetic rats, implying that UA could be a potential treatment for diabetic nephropathy.
doi:10.1016/j.curtheres.2013.07.001
PMCID: PMC3898186  PMID: 24465045
diabetic nephropathy; nuclear factor kappa-B; oxidative stress; ursolic acid
10.  LKB1 is a central regulator of tumor initiation and pro-growth metabolism in ErbB2-mediated breast cancer 
Cancer & Metabolism  2013;1:18.
Background
Germline and somatic mutations in STK11, the gene encoding the serine/threonine kinase LKB1, are strongly associated with tumorigenesis. While loss of LKB1 expression has been linked to breast cancer, the mechanistic role of LKB1 in regulating breast cancer development, metastasis, and tumor metabolism has remained unclear.
Methods
We have generated and analyzed transgenic mice expressing ErbB2 in the mammary epithelium of LKB1 wild-type or LKB1-deficient mice. We have also utilized ErbB2-expressing breast cancer cells in which LKB1 levels have been reduced using shRNA approaches. These transgenic and xenograft models were characterized for the effects of LKB1 loss on tumor initiation, growth, metastasis and tumor cell metabolism.
Results
We demonstrate that loss of LKB1 promotes tumor initiation and induces a characteristic shift to aerobic glycolysis (‘Warburg effect’) in a model of ErbB2-mediated breast cancer. LKB1-deficient breast cancer cells display enhanced early tumor growth coupled with increased cell migratory and invasive properties in vitro. We show that ErbB2-positive tumors deficient for LKB1 display a pro-growth molecular and phenotypic signature characterized by elevated Akt/mTOR signaling, increased glycolytic metabolism, as well as increased bioenergetic markers both in vitro and in vivo. We also demonstrate that mTOR contributes to the metabolic reprogramming of LKB1-deficient breast cancer, and is required to drive glycolytic metabolism in these tumors; however, LKB1-deficient breast cancer cells display reduced metabolic flexibility and increased apoptosis in response to metabolic perturbations.
Conclusions
Together, our data suggest that LKB1 functions as a tumor suppressor in breast cancer. Loss of LKB1 collaborates with activated ErbB2 signaling to drive breast tumorigenesis and pro-growth metabolism in the resulting tumors.
doi:10.1186/2049-3002-1-18
PMCID: PMC4178213  PMID: 24280377
Breast cancer; ErbB2; LKB1; Metabolism
11.  Limitations of Encapsidation of Recombinant Self-Complementary Adeno-Associated Viral Genomes in Different Serotype Capsids and Their Quantitation 
Human Gene Therapy Methods  2012;23(4):225-233.
Abstract
We previously reported that self-complementary adeno-associated virus (scAAV) type 2 genomes of up to 3.3 kb can be successfully encapsidated into AAV2 serotype capsids. Here we report that such oversized AAV2 genomes fail to undergo packaging in other AAV serotype capsids, such as AAV1, AAV3, AAV6, and AAV8, as determined by Southern blot analyses of the vector genomes, although hybridization signals on quantitative DNA slot-blots could still be obtained. Recently, it has been reported that quantitative real-time PCR assays may result in substantial differences in determining titers of scAAV vectors depending on the distance between the primer sets and the terminal hairpin structure in the scAAV genomes. We also observed that the vector titers determined by the standard DNA slot-blot assays were highly dependent on the specific probe being used, with probes hybridizing to the ends of viral genomes being significantly overrepresented compared with the probes hybridizing close to the middle of the viral genomes. These differences among various probes were not observed using Southern blot assays. This overestimation of titer is a systemic error during scAAV genome quantification, regardless of viral genome sequences and capsid serotypes. Furthermore, different serotypes capsid and modification of capsid sequence may affect the ability of packaging intact, full-length AAV genomes. Although the discrepancy is modest with wild-type serotype capsid and short viral genomes, the measured titer could be as much as fivefold different with capsid mutant vectors and large genomes. Thus, based on our data, we suggest that Southern blot analyses should be performed routinely to more accurately determine the titers of recombinant AAV vectors. At the very least, the use of probes/primers hybridizing close to the mutant inverted terminal repeat in scAAV genomes is recommended to avoid possible overestimation of vector titers.
Wang and colleagues report that 3.3 kb self-complementary (sc) AAV2 genomes fail to undergo packaging into AAV serotype capsids other than AAV2. Serotypes tested include AAV1, AAV3, AAV6, and AAV8. The authors also address the issue of qPCR titering assays leading to overestimation of scAAV vector titers and suggest Southern blot analyses as a more accurate and reliable titering method.
doi:10.1089/hgtb.2012.090
PMCID: PMC4015078  PMID: 22966785
12.  Evaluation of conservative treatment and timing of surgical intervention for mild forms of cervical spondylotic myelopathy 
The optimal management approach for patients with mild forms of cervical spondylotic myelopathy (MCSM) has not been well established. The aim of the present study was to investigate the outcome of conservative treatment, identify prognostic factors and provide evidence for the timing of surgical intervention. A total of 90 patients with MCSM attending hospital between February 2007 and January 2009 were prospectively enrolled. Initially, all patients received conservative treatment and were followed up periodically. When a deterioration in myelopathy was clearly identified, surgical treatment was conducted. Clinical and radiological factors correlating with the deterioration were examined, and final clinical outcomes were evaluated using the Japanese Orthopedic Association (JOA) score. At the end of January 2012, follow-ups of >3 years were completed. Seventy-eight patients were available for data analysis. Only 21 patients (26.9%) deteriorated and underwent surgery thereafter (group A), while the remaining 57 patients (73.1%) were treated conservatively throughout (group B). Statistical analysis revealed that segmental instability and cervical spinal stenosis were adverse factors for the prognosis of conservative treatment. Although the JOA scores of the patients in group A declined initially, following surgical intervention, no significant differences were identified in JOA scores between the two groups at the time of the final follow-up (P=0.46). In summary, conservative treatment is effective in MCSM patients. Patients with segmental instability and cervical spinal stenosis have a tendency to deteriorate, but conservative treatment remains the recommendation for the first action. If the myelopathy deteriorates during conservative treatment, timely surgical intervention is effective.
doi:10.3892/etm.2013.1224
PMCID: PMC3786935  PMID: 24137278
cervical myelopathy; conservative treatment; surgical treatment; prognosis
13.  A ubiquitin-binding protein FAAP20 links RNF8-mediated ubiquitination to the Fanconi anemia DNA Repair network 
Molecular Cell  2012;47(1):61-75.
SUMMARY
The Fanconi anemia (FA) protein network is necessary for repair of DNA interstrand crosslinks (ICLs), but its control mechanism remains unclear. Here we show that the network is regulated by a ubiquitin signaling cascade initiated by RNF8 and its partner, UBC13; and mediated by FAAP20, a component of the FA core complex. FAAP20 preferentially binds the ubiquitin product of RNF8-UBC13; and its recruitment to ICLs requires this ubiquitin-binding activity, RNF8 and UBC13. Both RNF8 and FAAP20 are required for recruitment of FA core complex and FANCD2 to ICLs, whereas RNF168 can modulate efficiency of the recruitment. RNF8 and FAAP20 are needed for efficient FANCD2 monoubiquitination, a key step of the FA network; RNF8 and FA core complex work in the same pathway to promote cellular resistance to ICLs. Thus, the RNF8-FAAP20 ubiquitin cascade is critical for recruiting FA core complex to ICLs and for normal function of the FA network.
doi:10.1016/j.molcel.2012.05.026
PMCID: PMC3398238  PMID: 22705371
RNF8; FAAP20; RNF168; UBC13; Fanconi Anemia; ubiquitin
14.  High-efficiency Transduction of Human Monocyte-derived Dendritic Cells by Capsid-modified Recombinant AAV2 Vectors 
Vaccine  2012;30(26):3908-3917.
Phosphorylation of surface-exposed tyrosine residues negatively impacts the transduction efficiency of recombinant AAV2 vectors. Pre-treatment of cells with specific cellular serine/threonine kinase inhibitors also significantly increased the transduction efficiency of AAV2 vectors. We reasoned that site-directed mutagenesis of surface-exposed serine residues might allow the vectors to evade phosphorylation and thus lead to higher transduction efficiency. Each of the 15 surface-exposed serine (S) residues was substituted with valine (V) residues, and the transduction efficiency of three of these mutants, S458V, S492Vand S662V, was increased by up to∼20-fold in different cell types. The S662V mutant was efficient in transducing human monocyte-derived dendritic cells (moDCs), a cell type not readily amenable to transduction by the conventional AAV vectors, and did not induce any phenotypic changes in these cells. Recombinant S662V-AAV2 vectors encoding a truncated human telomerase (hTERT) gene were generated and used to stimulate cytotoxic T cells (CTLs) against target cells. S662V-AAV2-hTERT vector-transduced DCs resulted in rapid, specific T-cell clone proliferation and generation of robust CTLs, which led to specific cell lysis of K562 cells. These studies suggest that high-efficiency transduction of moDCs by serine-modified AAV2 vectors is feasible, which supports the potential utility of these vectors for future human DC vaccine studies.
doi:10.1016/j.vaccine.2012.03.079
PMCID: PMC3356484  PMID: 22497875
adeno-assosiated virus vectors; capsid proteins; serine-phosphorylation; serine/threonine kinase; dendritic cells; gene expression
15.  Optimization of the Capsid of Recombinant Adeno-Associated Virus 2 (AAV2) Vectors: The Final Threshold? 
PLoS ONE  2013;8(3):e59142.
The ubiquitin-proteasome pathway plays a critical role in the intracellular trafficking of AAV2 vectors, and phosphorylation of certain surface-exposed amino acid residues on the capsid provides the primary signal for ubiquitination. Removal of several critical tyrosine (Y) and serine (S) residues on the AAV2 capsid has been shown to significantly increase transduction efficiency compared with the wild-type (WT) vectors. In the present study, site-directed mutagenesis of each of the 17 surface-exposed threonine (T) residues was conducted, and the transduction efficiency of four of these mutants, T455V, T491V, T550V, and T659V, was observed to increase up to 4-fold in human HEK293 cells in vitro. The most critical Y, S, and T mutations were subsequently combined, and the quadruple-mutant (Y444+500+730F+T491V) AAV2 vector was identified as the most efficient. This vector increased the transduction efficiency ∼24-fold over the WT AAV2 vector, and ∼2–3-fold over the previously described triple-mutant (Y444+500+730F) vector in a murine hepatocyte cell line, H2.35, in vitro. Similar results were obtained in murine hepatocytes in vivo following tail vein injection of the Y444+500+730F+T491V scAAV2 vector, and whole-body bioluminescence imaging of C57BL/6 mice. The increase in the transduction efficiency of the Y-T quadruple-mutant over that of the Y triple-mutant correlated with an improved nuclear translocation of the vectors, which exceeded 90%. These observations suggest that further optimization of the AAV2 capsid by targeting amino acid residues involved in phosphorylation may not be possible. This study has thus led to the generation of a novel Y444+500+730F+T491V quadruple-mutant AAV2 vector with potential for use in liver-directed human gene therapy.
doi:10.1371/journal.pone.0059142
PMCID: PMC3602601  PMID: 23527116
16.  High-Efficiency Transduction of Primary Human Hematopoietic Stem Cells and Erythroid Lineage-Restricted Expression by Optimized AAV6 Serotype Vectors In Vitro and in a Murine Xenograft Model In Vivo 
PLoS ONE  2013;8(3):e58757.
We have observed that of the 10 AAV serotypes, AAV6 is the most efficient in transducing primary human hematopoietic stem cells (HSCs), and that the transduction efficiency can be further increased by specifically mutating single surface-exposed tyrosine (Y) residues on AAV6 capsids. In the present studies, we combined the two mutations to generate a tyrosine double-mutant (Y705+731F) AAV6 vector, with which >70% of CD34+ cells could be transduced. With the long-term objective of developing recombinant AAV vectors for the potential gene therapy of human hemoglobinopathies, we generated the wild-type (WT) and tyrosine-mutant AAV6 vectors containing the following erythroid cell-specific promoters: β-globin promoter (βp) with the upstream hyper-sensitive site 2 (HS2) enhancer from the β-globin locus control region (HS2-βbp), and the human parvovirus B19 promoter at map unit 6 (B19p6). Transgene expression from the B19p6 was significantly higher than that from the HS2-βp, and increased up to 30-fold and up to 20-fold, respectively, following erythropoietin (Epo)-induced differentiation of CD34+ cells in vitro. Transgene expression from the B19p6 or the HS2-βp was also evaluated in an immuno-deficient xenograft mouse model in vivo. Whereas low levels of expression were detected from the B19p6 in the WT AAV6 capsid, and that from the HS2-βp in the Y705+731F AAV6 capsid, transgene expression from the B19p6 promoter in the Y705+731F AAV6 capsid was significantly higher than that from the HS2-βp, and was detectable up to 12 weeks post-transplantation in primary recipients, and up to 6 additional weeks in secondary transplanted animals. These data demonstrate the feasibility of the use of the novel Y705+731F AAV6-B19p6 vectors for high-efficiency transduction of HSCs as well as expression of the b-globin gene in erythroid progenitor cells for the potential gene therapy of human hemoglobinopathies such as β-thalassemia and sickle cell disease.
doi:10.1371/journal.pone.0058757
PMCID: PMC3597592  PMID: 23516552
17.  Development of optimized AAV3 serotype vectors: Mechanism of high-efficiency transduction of human liver cancer cells 
Gene therapy  2011;19(4):375-384.
Our recent studies have revealed that among the 10 different commonly used AAV serotypes, AAV3 vectors transduce human liver cancer cells extremely efficiently because these cells express high levels of human hepatocyte growth factor receptor (hHGFR), and AAV3 utilizes hHGFR as a cellular co-receptor for viral entry. In this report, we provide further evidence that both extracellular as well as intracellular kinase domains of hHGFR are involved in AAV3 vector entry and AAV3-mediated transgene expression. We also document that AAV3 vectors are targeted for degradation by the host cell proteasome machinery, and that site-directed mutagenesis of surface exposed tyrosine (Y) to phenylalanine (F) residues on AAV3 capsids significantly improves the transduction efficiency of Y701F, Y705F and Y731F mutant AAV3 vectors. The transduction efficiency of the Y705+731F double-mutant vector is significantly higher than each of the single-mutants in liver cancer cells in vitro. In immuno-deficient mouse xenograft models, direct intra-tumor injection of AAV3 vectors also led to high-efficiency transduction of human liver tumor cells in vivo. We also document here that the optimized tyrosine-mutant AAV3 vectors lead to increased transduction efficiency following both intra-tumor and tail-vein injections in vivo. The optimized tyrosine-mutant AAV3 serotype vectors containing pro-apoptotic genes should prove useful for the potential gene therapy of human liver cancers.
doi:10.1038/gt.2011.105
PMCID: PMC3519243  PMID: 21776025
AAV vectors; tyrosine mutants; human hepatocyte growth factor receptor; human liver cancer; gene therapy
18.  A Simple Method to Increase the Transduction Efficiency of Single-Stranded Adeno-Associated Virus Vectors In Vitro and In Vivo 
Human Gene Therapy  2011;22(5):633-640.
Abstract
We have recently shown that co-administration of conventional single-stranded adeno-associated virus 2 (ssAAV2) vectors with self-complementary (sc) AAV2-protein phosphatase 5 (PP5) vectors leads to a significant increase in the transduction efficiency of ssAAV2 vectors in human cells in vitro as well as in murine hepatocytes in vivo. In the present study, this strategy has been further optimized by generating a mixed population of ssAAV2-EGFP and scAAV2-PP5 vectors at a 10:1 ratio to achieve enhanced green fluorescent protein (EGFP) transgene expression at approximately 5- to 10-fold higher efficiency, both in vitro and in vivo. This simple coproduction method should be adaptable to any ssAAV serotype vector containing transgene cassettes that are too large to be encapsidated in scAAV vectors.
Previous studies by this group have shown that coadministration of conventional single-stranded adenoassociated virus serotype 2 (ssAAV2) vectors with self-complementary (sc) AAV2–protein phosphatase-5 (PP5) vectors leads to a significant increase in the transduction efficiency of ssAAV2 vectors in human cells in vitro as well as in murine hepatocytes in vivo. Here, Ma and colleagues expand on those previous findings and describe a quadruple-plasmid transfection protocol that results in the production of ssAAV vectors that transduce cells up to 9-fold more efficiently than in the absence of PP5 coexpression.
doi:10.1089/hum.2010.243
PMCID: PMC3081437  PMID: 21219084
19.  Transplantation of insulin-producing cells from umbilical cord mesenchymal stem cells for the treatment of streptozotocin-induced diabetic rats 
Background
Although diabetes mellitus (DM) can be treated with islet transplantation, a scarcity of donors limits the utility of this technique. This study investigated whether human mesenchymal stem cells (MSCs) from umbilical cord could be induced efficiently to differentiate into insulin-producing cells. Secondly, we evaluated the effect of portal vein transplantation of these differentiated cells in the treatment of streptozotocin-induced diabetes in rats.
Methods
MSCs from human umbilical cord were induced in three stages to differentiate into insulin-producing cells and evaluated by immunocytochemistry, reverse transcriptase, and real-time PCR, and ELISA. Differentiated cells were transplanted into the liver of diabetic rats using a Port-A catheter via the portal vein. Blood glucose levels were monitored weekly.
Results
Human nuclei and C-peptide were detected in the rat liver by immunohistochemistry. Pancreatic β-cell development-related genes were expressed in the differentiated cells. C-peptide release was increased after glucose challenge in vitro. Furthermore, after transplantation of differentiated cells into the diabetic rats, blood sugar level decreased. Insulin-producing cells containing human C-peptide and human nuclei were located in the liver.
Conclusion
Thus, a Port-A catheter can be used to transplant differentiated insulin-producing cells from human MSCs into the portal vein to alleviate hyperglycemia among diabetic rats.
doi:10.1186/1423-0127-19-47
PMCID: PMC3404952  PMID: 22545626
Mesenchymal stem cell; Portal vein; Insulin-producing cells; Transplant
20.  Human Hepatocyte Growth Factor Receptor Is a Cellular Coreceptor for Adeno-Associated Virus Serotype 3 
Human Gene Therapy  2010;21(12):1741-1747.
Ling et al. identify human hepatocyte growth factor (hHGFR) as a novel receptor/coreceptor necessary for AAV3 entry into liver-specific cells. Using a variety of methods, the authors show that interference with the cell surface expression of HGFR significantly reduces the transduction efficiency of AAV3 vectors. Subsequent in vitro and in vivo experiments revealed that AAV3 specifically utilizes human HGFR (hHGFR), and not mouse HGFR (mHGFR).
Abstract
Adeno-associated viruses (AAVs) use a variety of cellular receptors/coreceptors to gain entry into cells. A number of AAV serotypes are now available, and the cognate receptors/coreceptors for only a handful of those have been identified thus far. Of the 10 commonly used AAV serotypes, AAV3 is by far the least efficient in transducing cells in general. However, in our more recent studies, we observed that AAV3 vectors transduced human liver cancer cells remarkably well, which led to the hypothesis that AAV3 uses hepatocyte growth factor receptor (HGFR) as a cellular coreceptor for viral entry. AAV3 infection of human liver cancer cell lines was strongly inhibited by hepatocyte growth factor, HGFR-specific small interfering RNA, and anti-HGFR antibody, which corroborated this hypothesis. However, AAV3 vectors failed to transduce murine hepatocytes, both in vitro and in vivo, suggesting that AAV3 specifically uses human HGFR, but not murine HGFR, as a cellular coreceptor for transduction. AAV3 may prove to be a useful vector for targeting human liver cancers for the potential gene therapy.
doi:10.1089/hum.2010.075
PMCID: PMC2999576  PMID: 20545554
21.  High-Efficiency Transduction of Fibroblasts and Mesenchymal Stem Cells by Tyrosine-Mutant AAV2 Vectors for Their Potential Use in Cellular Therapy 
Human Gene Therapy  2010;21(11):1527-1543.
Previous reports have shown that site-directed mutagenesis of surface-exposed tyrosine residues on the capsid of AAV2 leads to enhanced transduction efficiency. In this report, Li and colleagues use these AAV2 tyrosine mutants and demonstrate that they are capable of transducing up to 90% of mouse and human bone marrow derived mesenchymal stem cells.
Abstract
Adeno-associated virus 2 (AAV2) vectors transduce fibroblasts and mesenchymal stem cells (MSCs) inefficiently, which limits their potential widespread applicability in combinatorial gene and cell therapy. We have reported that AAV2 vectors fail to traffic efficiently to the nucleus in murine fibroblasts. We have also reported that site-directed mutagenesis of surface-exposed tyrosine residues on viral capsids leads to improved intracellular trafficking of the mutant vectors, and the transduction efficiency of the single tyrosine-mutant vectors is ∼10-fold higher in human cells. In the current studies, we evaluated the transduction efficiency of single as well as multiple tyrosine-mutant AAV2 vectors in murine fibroblasts. Our results indicate that the Y444F mutant vectors transduce these cells most efficiently among the seven single-mutant vectors, with >30-fold increase in transgene expression compared with the wild-type vectors. When the Y444F mutation is combined with additional mutations (Y500F and Y730F), the transduction efficiency of the triple-mutant vectors is increased by ∼130-fold and the viral intracellular trafficking is also significant improved. Similarly, the triple-mutant vectors are capable of transducing up to 80–90% of bone marrow-derived primary murine as well as human MSCs. Thus, high-efficiency transduction of fibroblasts with reprogramming genes to generate induced pluripotent stem cells, and the MSCs for delivering therapeutic genes, should now be feasible with the tyrosine-mutant AAV vectors.
Overview Summary
Fibroblasts and mesenchymal stem cells (MSCs) are promising targets for gene and cell therapy. Recombinant adeno-associated virus 2 (AAV2) vectors are currently in use in several Phase I/II clinical trials for gene therapy. However, the existing data show that AAV2 vector-mediated transduction of fibroblasts and MSCs is inefficient. We observed that AAV2 vectors containing mutations in three surface-exposed tyrosine residues significantly increase transduction efficiency in fibroblasts, as well as in both human and murine primary MSCs. The increased transduction efficiency of these triple-mutant AAV2 vectors correlates well with improved viral intracellular trafficking in fibroblasts. These data provide strong evidence that high-efficiency gene delivery and transgene expression by AAV vectors are indeed feasible, which should facilitate the generation of induced pluripotent stem cells, as well as the use of MSCs in combinatorial gene and cell therapy.
doi:10.1089/hum.2010.005
PMCID: PMC2987376  PMID: 20507237
22.  A histone-fold complex and FANCM form a conserved DNA remodeling complex to maintain genome stability 
Molecular cell  2010;37(6):865-878.
SUMMARY
FANCM remodels branched DNA structures and plays essential roles in the cellular response to DNA replication stress. Here we show that FANCM forms a conserved DNA remodeling complex with a histone-fold heterodimer, MHF. We find that MHF stimulates DNA binding and replication fork remodeling by FANCM. In the cell, FANCM and MHF are rapidly recruited to forks stalled by DNA interstrand crosslinks, and both are required for cellular resistance to such lesions. In vertebrates, FANCM-MHF associates with the Fanconi anemia (FA) core complex, promotes FANCD2 monoubiquitination in response to DNA damage, and suppresses sister-chromatid exchanges. Yeast orthologs of these proteins function together to resist MMS-induced DNA damage and promote gene conversion at blocked replication forks. Thus, FANCM-MHF is an essential DNA remodeling complex that protects replication forks from yeast to human.
doi:10.1016/j.molcel.2010.01.039
PMCID: PMC2847587  PMID: 20347428
FANCM; Fanconi Anemia; DNA repair; Histone fold; CENP-S; CENP-X
23.  High-Efficiency Transduction of Liver Cancer Cells by Recombinant Adeno-Associated Virus Serotype 3 Vectors  
Recombinant vectors based on a non-pathogenic human parvovirus, the adeno-associated virus 2 (AAV2) have been developed, and are currently in use in a number of gene therapy clinical trials. More recently, a number of additional AAV serotypes have also been isolated, which have been shown to exhibit selective tissue-tropism in various small and large animal models1. Of the 10 most commonly used AAV serotypes, AAV3 is by far the least efficient in transducing cells and tissues in vitro as well as in vivo.
However, in our recently published studies, we have documented that AAV3 vectors transduce human liver cancer - hepatoblastoma (HB) and hepatocellular carcinoma (HCC) - cell lines extremely efficiently because AAV3 utilizes human hepatocyte growth factor receptor as a cellular co-receptor for binding and entry in these cells2,3.
In this article, we describe the steps required to achieve high-efficiency transduction of human liver cancer cells by recombinant AAV3 vectors carrying a reporter gene. The use of recombinant AAV3 vectors carrying a therapeutic gene may eventually lead to the potential gene therapy of liver cancers in humans.
doi:10.3791/2538
PMCID: PMC3197307  PMID: 21445055
24.  Mirror-Image Arachnoid Cysts in a Pair of Monozygotic Twins: A Case Report and Review of the Literature 
Mirror-imaging of arachnoid cysts (ACs) in monozygotic twins (MZ) is extremely rare. We describe a pair of MZ who developed mirror-imaging of ACs in the temporal fossas, and we also review the literature. Brain computer tomography (CT) and Magnetic Resonance Imaging (MRI) of the MZ revealed mirror-imaging of vast lesions of cerebrospinal fluid intensity in their temporal fossas. This is the second ever report of such a case according to the available literature. Unlike the prior case, our patients were 14 months, which is a much younger age than the patients of the previous report. Consequently, our case is better in supporting a genetic origin in the pathogenesis of AC. The findings in our case indicate that early neuroimaging is mandatory in the counterpart of the symptomatic patient with AC, irrespective of the absence of symptoms.
PMCID: PMC3133845  PMID: 21750644
Mirror image; Arachnoid cyst; Monozygotic twins
25.  14-3-3ζ Cooperates with ErbB2 to Promote Progression of Ductal Carcinoma in Situ to Invasive Breast Cancer by Inducing Epithelial-Mesenchymal Transition 
Cancer cell  2009;16(3):195-207.
Summary
ErbB2, a metastasis-promoting oncoprotein, is overexpressed in ~25% of invasive/metastatic breast cancers, but in 50–60% of non-invasive ductal carcinomas in situ (DCIS). It has been puzzling how a subset of ErbB2-overexpressing DCIS develops into invasive breast cancer (IBC). We found that co-overexpression of 14-3-3ζ in ErbB2-overexpressing DCIS conferred a higher risk of progression to IBC. ErbB2 and 14-3-3ζ overexpression, respectively, increased cell migration and decreased cell adhesion, two prerequisites of tumor cell invasion. 14-3-3ζ overexpression reduced cell adhesion by activating the TGFβ/Smads pathway that led to ZFHX1B/SIP-1 upregulation, E-cadherin loss, and epithelial-mesenchymal transition (EMT). Importantly, patients whose breast tumors overexpressed both ErbB2 and 14-3-3ζ had higher rates of metastatic recurrence and death than those whose tumors overexpressed only one.
doi:10.1016/j.ccr.2009.08.010
PMCID: PMC2754239  PMID: 19732720

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