Nutritional control of epigenetic processes in yeast and human cells

The vitamin folate is required for methionine homeostasis in all organisms. In addition to its role in protein synthesis, methionine is the precursor to S-adenosyl-methionine (SAM), which is used in myriad cellular methylation reactions, including all histone methylation reactions. Here, we demonstrate that folate and methionine deficiency led to reduced methylation of lysine 4 of histone H3 (H3K4) in Saccharomyces cerevisiae. The effect of nutritional deficiency on H3K79 methylation was less pronounced, but was exacerbated in S. cerevisiae carrying a hypomorphic allele of Dot1, the enzyme responsible for H3K79 methylation. This result suggested a hierarchy of epigenetic modifications in terms of their susceptibility to nutritional limitations. Folate deficiency caused changes in gene transcription that mirrored the effect of complete loss of H3K4 methylation. Histone methylation was also found to respond to nutritional deficiency in the fission yeast Schizosaccharomyces pombe and in human cells in culture.

Targeting IL-23 by employing a p40 peptide-based vaccine ameliorates murine allergic skin and airway inflammation

BACKGROUND

Studies have found that the IL-23/Th17 pathway plays an important role in the pathogenesis of atopic dermatitis (AD) and severe and steroid-resistant asthma. Targeting IL-23/Th17 pathway with monoclonal antibodies (mAb) has been successful in the reduction of skin and airway inflammation in animal models. However, the mAb has a short half-life, requiring repeated administrations. For the long-term suppression of IL-23/Th17 pathway, we have previously developed an IL-23p40 peptide-based virus-like particle vaccine, which induces long-lasting autoantibodies to IL-23.

OBJECTIVE

We sought to evaluate the effects of this IL-23p40 peptide-based vaccine on the down-regulation of allergic skin and airway inflammation in mice.

METHODS

Mice were subcutaneously injected three times with the IL-23p40 vaccine, or the vaccine carrier protein or saline as controls. Two weeks later, mice were epicutaneously sensitized with ovalbumin four times at a 2-week interval. One week after the final sensitization, mice were nasally administrated with ovalbumin daily for 3 days. One day later, bronchoalveolar lavage fluids (BALF), sera, lung and skin tissues were obtained and analysed.

RESULTS

Mice immunized with the vaccine produced high levels of IgG antibodies to IL-23, p40 and IL-12 that in vitro inhibited IL-23-dependent IL-17 production. The numbers of total cells, neutrophils, and eosinophils in BALF were significantly reduced in the vaccine group, compared with controls. The levels of IL-13, IL-5, IL-23 and, IL-17 in BALF and levels of serum ovalbumin-specific IgE, IgG1, and total IgE were also significantly decreased. Histological analysis showed less inflammation of the lung and skin tissues in the vaccine group, compared with controls.

CONCLUSION AND CLINICAL RELEVANCE

Administration of an IL-23p40 peptide-based vaccine down-regulates allergic skin and airway inflammation, suggesting that this strategy may be a potential therapeutic approach in the treatment of AD and asthma.

Dissection of the maternal effects on puberty onset by embryo transplantation in mouse

Puberty onset in mammals is affected by multiple genetic and environmental factors. Among which, the maternal effect could have played a considerable role. In our previous study, we found that the F1 offspring from reciprocal crosses between C3H/HeJ (C3H) and C57BL/6J (B6) mice differed significantly in the timing of puberty in both sexes, though they had identical genomic background. In order to dissect the causative factors to such phenomenon of maternal effect, embryos from reciprocal crosses of C3H/HeJ and C57BL/6J mice were collected and transplanted to the uterus of either strain of mothers, and the puberty onset of pups were compared between different recipient mothers and egg origins. The results showed that the male pups from C3H recipient mothers attained puberty onset earlier than those from B6 recipients significantly, while the female pups did not show such difference. On the other hand, the egg origin made no difference in the puberty onset of either sex, yet it influenced the birth weight of female pups significantly (p<0.05). The manipulation of embryo transplantation delayed the puberty onset of pups dramatically. A mitochondria substitution strain between B6 and C3H (BmC), which had the genome background of B6 and a mitochondrial hyplotype of C3H, had the same phenotype of puberty onset as B6. The integrated results indicated that the uterine environment was the major causative factors to the maternal effect on the differential puberty onset in reciprocal crosses of F1 hybrids between B6 and C3H mice.

Multiple means to the same end: the genetic basis of acquired stress resistance in yeast

In nature, stressful environments often occur in combination or close succession, and thus the ability to prepare for impending stress likely provides a significant fitness advantage. Organisms exposed to a mild dose of stress can become tolerant to what would otherwise be a lethal dose of subsequent stress; however, the mechanism of this acquired stress tolerance is poorly understood. To explore this, we exposed the yeast gene-deletion libraries, which interrogate all essential and non-essential genes, to successive stress treatments and identified genes necessary for acquiring subsequent stress resistance. Cells were exposed to one of three different mild stress pretreatments (salt, DTT, or heat shock) and then challenged with a severe dose of hydrogen peroxide (H₂O₂). Surprisingly, there was little overlap in the genes required for acquisition of H₂O₂ tolerance after different mild-stress pretreatments, revealing distinct mechanisms of surviving H₂O₂ in each case. Integrative network analysis of these results with respect to protein–protein interactions, synthetic–genetic interactions, and functional annotations identified many processes not previously linked to H₂O₂ tolerance. We tested and present several models that explain the lack of overlap in genes required for H₂O₂ tolerance after each of the three pretreatments. Together, this work shows that acquired tolerance to the same severe stress occurs by different mechanisms depending on prior cellular experiences, underscoring the context-dependent nature of stress tolerance.

Cells experience stressful conditions in the real world that can threaten physiology. Therefore, organisms have evolved intricate defense systems to protect themselves against environmental stress. Many organisms can increase their stress tolerance at the first sign of a problem through a phenomenon called acquired stress resistance: when pre-exposed to a mild dose of one stress, cells can become super-tolerant to subsequent stresses that would kill unprepared cells. This response is observed in many organisms, from bacteria to plants to humans, and has application in human health and disease treatment; however, its mechanism remains poorly understood. We used yeast as a model to identify genes important for acquired resistance to severe oxidative stress after pretreatment with three different mild stresses (osmotic, heat, or reductive shock). Surprisingly, there was little overlap in the genes required to survive the same severe stress after each pretreatment. This reveals that the mechanism of acquiring tolerance to the same severe stress occurs through different routes depending on the mild stressor. We leveraged available datasets of physical and genetic interaction networks to address the mechanism and regulation of stress tolerance. We find that acquired stress resistance is a unique phenotype that can uncover new insights into stress biology.

Autologous hematopoietic cell transplantation following high-dose immunosuppressive therapy for advanced multiple sclerosis: long-term results

The purpose of the study was to determine the long-term safety and effectiveness of high-dose immunosuppressive therapy (HDIT) followed by autologous hematopoietic cell transplantation (AHCT) in advanced multiple sclerosis (MS). Total body irradiation, cyclophosphamide, and antithymocyte globulin were followed by transplantation of autologous, CD34-selected peripheral blood stem cells (PBSC). Neurological examinations, brain MRIs and cerebrospinal fluid (CSF) for oligoclonal bands (OCB) were serially evaluated. Patients (n=26, mean EDSS=7.0, 17 secondary progressive, 8 primary progressive, 1 relapsing/remitting) were followed for a median of 48 months after HDIT followed by AHCT. The 72-month probability of worsening ≥ 1.0 EDSS point was 0.52 (95% CI, 0.30 to 0.75). Five patients had an EDSS at baseline of ≤ 6.0; four of these had not failed treatment at last study visit. OCB in CSF persisted with minor changes in the banding pattern. Four new or enhancing lesions were seen on MRI, all within 13 months of treatment. In this population with high baseline EDSS, a significant proportion of patients with advanced MS remained stable as long as 7 years after transplant. Non-inflammatory events may have contributed to neurological worsening after treatment. HDIT/AHCT may be more effective in patients with less advanced relapsing/remitting MS.

Cloning expression, monoclonal antibody preparation and serologic study of mammaglobin in breast cancer

Mammaglobin may be a potential serum biomarker for the differential diagnosis of breast cancer. 260 serum samples were collected from 127 untreated breast cancer patients and 133 healthy volunteers to analyze the sera expression of mammaglobin and its implications for both. The expression vector of pGEX-4T-2-Mammaglobin and pBVIL1-Mammaglobin were constructed and transformed into E.coli.HB101 for expression. The mice were immunized with the purified recombinant protein to prepare monoclonal antibody and to detect by ELISA the serum of normal people and breast cancer patients. Recombinant mammaglobin antigen was effectively expressed in E.coli. Two hybridoma cell lines were obtained after the mice were immunized by pGEX-4T-2-mammaglobin. 133 cases of normal serum and 127 cases of breast cancer serum were analyzed by ELISA. The sera expression level of mammaglobin in breast cancer group (average OD value 0.645±0.223) was significantly (p

KEYWORDS

mammaglobin; cloning expression; monoclonal antibody; serologic study; breast cancer.

Regression to normoglycaemia by fenofibrate in pre-diabetic subjects complicated with hypertriglyceridaemia: a prospective randomized controlled trial

AIMS

Lipotoxicity has recently been shown to be an important risk factor underlying the pathogenesis of pre-diabetes. However, clinical evidence supporting the treatment of pre-diabetes by improving lipotoxicity is lacking. Here, we conducted an open-label, randomized, controlled trial to investigate whether fenofibrate, the widely used hypolipidaemic agent, might benefit pre-diabetes, with metformin and diet control, the recommended intervention methods, as positive controls.

METHODS

Newly diagnosed pre-diabetes patients (n = 120) with hypertriglyceridaemia (plasma triglyceride levels between 1.8 and 4.5 mmol/l) were randomly assigned by computer-generated randomization sequence to either control group (no intervention), fenofibrate group (200 mg once a day), metformin group (500 mg three times a day) or diet-controlled group (diet recommendation). Plasma biochemistry examination was performed every 2 months. The primary endpoint was the outcome of the natural course of pre-diabetes, evaluated by oral glucose tolerance test after 6-month follow-up.

RESULTS

Twenty subjects in the fenofibrate group, 24 subjects in the metformin group and 25 subjects in both the diet-controlled group and the control group finished the trial. Fenofibrate, metformin and diet control had protective effects on hypertriglyceridaemic pre-diabetes, evidenced by 53.3, 70 and 30% participants regressed to normoglycaemia, respectively. The effects of fenofibrate and metformin were comparable (P > 0.05), while diet control was less effective (P < 0.05). Liver damage occurred in six subjects in the fenofibrate group and gastrointestinal symptoms occurred in four subjects in the metformin group. No serious adverse events occurred.

CONCLUSION

Controlling lipotoxicity by fenofibrate could effectively ameliorate the natural course of hypertriglyceridaemic pre-diabetes.

New clinical features of thyroid cancer in eastern China

OBJECTIVE

Analyze recent clinical features of thyroid cancer in eastern China.

METHODS

Investigation and comparison of clinical data of thyroid cancer patients from 1996 to 2006 from the Department of Head and Neck Surgery in the Cancer Hospital of Fudan University, Shanghai, China.

RESULTS

The number of patients with thyroid cancer rose from 148 in the year 1996 to 572 in the year 2006, a 3.9-fold increase. Routine ultrasound survey during physical examination revealed four cases (2.7%) in 1996 and 285 cases (49.8%) in 2006. The sensitivity of the ultrasound survey in thyroid cancer diagnosis was 86.66% in 1996 and 88.20% in 2006 (P>0.05). Papillary carcinoma was most prevalent (87.8% in 1996 and 92.8% in 2006). An increasing proportion of small tumors was found. The incidence of microcarcinoma was 35.7% in 2006 in contrast with 20.3% in 1996 (P<0.01). Moreover, tumors with diameter from 1 to 2 cm were found in 38.5% patients in 2006 as opposed to 27.0% in 1996 (P<0.01). Extrathyroid extension was reported in 46 (31.1%) patients in 1996, but only in 39 (6.8%) in 2006 (P<0.01). Central cervical lymph node metastases were found in 98 (66.2%) patients in 1996, contrasting with 301 (52.6%) in 2006 (P<0.05). Thirty-seven (25.0%) patients had lateral cervical lymph node metastasis in 1996 compared with 117 (20.5%) in 2006 (P>0.05). Last, the proportion of stage I cancers in 2006 was higher than that in 1996.

CONCLUSION

With the increasing incidence of thyroid cancer, cancer was discovered at an earlier stage. This is due to new clinical features of thyroid cancer, such as the decrease in tumor diameter, the lower rate of extrathyroid extension and of cervical lymph node metastasis. Routine ultrasound survey during physical examination has become the most common way to detect thyroid cancer. Increasing usage of diagnostic scrutiny, including the ultrasound survey, has most likely contributed to the increased incidence through detection of small thyroid cancers. Increased use of ultrasound to screen thyroid cancer in early stages should lead to better therapeutic outcome.

NOS2 (iNOS) deficiency in kidney donor accelerates allograft loss in a murine model

Renal NOS2 is expressed and produces abundant nitric oxide (NO) in various renal cells in response to proinflammatory cytokines. However, the role of this enzyme in renal allograft survival remains unknown. Kidney allotransplantation was performed in the murine model of C57BL/6J (H-2(d)) to nephrectomized Balb/c (H-2(b)) mice. Here we show that deficiency in NOS2 expression in kidney donors significantly advanced allograft failure, indicated by decreasing mean survival of recipients receiving NOS2 null grafts (15.4 +/- 6.4 days) as compared to those with wild type grafts (65.4 +/- 28.1 days) (p = 0.0005). Consistent with survival results, NOS2 null grafts had more severe renal tubule injury and decreased renal function compared to wild type grafts. In vitro NOS2 expressing TEC had greater resistance to allogeneic lymphocyte-mediated apoptosis. The addition of exogenous NO inhibited Fas-mediated TEC apoptosis and reduced proliferation of allogeneic lymphocytes. These data suggest that endogenous production of NO through renal NOS2 activity can play a protective role in kidney grafts through attenuating Fas-mediated donor cell apoptosis as well as by inhibiting proliferation of inflammatory infiltrating lymphocytes. Enhanced donor NOS2 expression may be a useful strategy to improve kidney transplant survival.

Impact of nonsense-mediated mRNA decay on the global expression profile of budding yeast

Nonsense-mediated mRNA decay (NMD) is a eukaryotic mechanism of RNA surveillance that selectively eliminates aberrant transcripts coding for potentially deleterious proteins. NMD also functions in the normal repertoire of gene expression. In Saccharomyces cerevisiae, hundreds of endogenous RNA Polymerase II transcripts achieve steady-state levels that depend on NMD. For some, the decay rate is directly influenced by NMD (direct targets). For others, abundance is NMD-sensitive but without any effect on the decay rate (indirect targets). To distinguish between direct and indirect targets, total RNA from wild-type (Nmd⁺) and mutant (Nmd⁻) strains was probed with high-density arrays across a 1-h time window following transcription inhibition. Statistical models were developed to describe the kinetics of RNA decay. 45% ± 5% of RNAs targeted by NMD were predicted to be direct targets with altered decay rates in Nmd⁻ strains. Parallel experiments using conventional methods were conducted to empirically test predictions from the global experiment. The results show that the global assay reliably distinguished direct versus indirect targets. Different types of targets were investigated, including transcripts containing adjacent, disabled open reading frames, upstream open reading frames, and those prone to out-of-frame initiation of translation. Known targeting mechanisms fail to account for all of the direct targets of NMD, suggesting that additional targeting mechanisms remain to be elucidated. 30% of the protein-coding targets of NMD fell into two broadly defined functional themes: those affecting chromosome structure and behavior and those affecting cell surface dynamics. Overall, the results provide a preview for how expression profiles in multi-cellular eukaryotes might be impacted by NMD. Furthermore, the methods for analyzing decay rates on a global scale offer a blueprint for new ways to study mRNA decay pathways in any organism where cultured cell lines are available.

Genes determine the structure of proteins through transcription and translation in which an RNA copy of the gene is made (mRNA) and then translated to make the protein. Cellular protein levels reflect the relative rates of mRNA synthesis and degradation, which are subject to multiple layers of controls. Mechanisms also exist to ensure the quality of each mRNA. One quality control mechanism called nonsense-mediated mRNA decay (NMD) triggers the rapid degradation of mRNAs containing coding errors that would otherwise lead to the production of non-functional or potentially deleterious proteins. NMD occurs in yeasts, plants, flies, worms, mice, and humans. In humans, NMD affects the etiology of genetic disorders by affecting the expression of genes that carry disease-causing mutations. Besides quality assurance, NMD plays another role in gene expression by controlling the abundance of hundreds of normal mRNAs that are devoid of coding errors. In this paper, the authors used DNA arrays to monitor the relative decay rates of all mRNAs in budding yeast and found a subset where decay rates were dependent on NMD. Many of the corresponding proteins perform related functional roles affecting both the structure and behavior of chromosomes and the structure and integrity of the cell surface.

Increasing resistance of tubular epithelial cells to apoptosis by shRNA therapy ameliorates renal ischemia-reperfusion injury

Renal tubular epithelial cells (TEC) die by apoptosis or necrosis in renal ischemia-reperfusion injury (IRI). Fas/Fas ligand-dependent fratricide is critical in TEC apoptosis, and Fas promotes renal IRI. Therefore, targeting Fas or caspase-8 may have therapeutic potential for renal injury in kidney transplant or failure. RNA silencing by short hairpin RNA (shRNA) is a novel strategy to down-regulate protein expression. Using this approach, silencing of Fas or caspase-8 by shRNA to prevent TEC apoptosis and IRI was evaluated. IRI was induced by renal artery clamping for 45 or 60 min at 32 degrees C in uninephrectomized C57BL/6 mice. Here, we showed that Fas or pro-caspase-8 expression was significantly knocked down in TEC by stable expression of shRNA, resulting in resistance to apoptosis induced by superoxide, IFN-gamma/TNF-alpha and anti-Fas antibody. Inferior vena cava delivery of pHEX-small interfering RNA targeting Fas or pro-caspase-8 resulted in protection of kidney from IRI, indicated by reduction of renal tubular injury (necrosis and apoptosis) and serum creatinine or blood urea nitrogen. Our data suggest that shRNA-based therapy targeting Fas and caspase-8 in renal cells can lead to protection of kidney from IRI. Attenuation of pro-apoptotic proteins using genetic manipulation strategies such as shRNA might represent a novel strategy to promote kidney allograft survival from rejection or failure.

Ebs1p, a negative regulator of gene expression controlled by the Upf proteins in the yeast Saccharomyces cerevisiae

Mutations in EBS1 were identified in Saccharomyces cerevisiae that cosuppress missense, frameshift, and nonsense mutations. Evidence from studies of loss of function and overexpression of EBS1 suggests that Ebs1p affects gene expression by inhibiting translation and that a loss of EBS1 function causes suppression by increasing the rate of translation. Changes in EBS1 expression levels alter the expression of wild-type genes, but, in general, no changes in mRNA abundance were associated with a loss of function or overexpression of EBS1. Translation of a lacZ reporter was increased in strains carrying an ebs1-Delta mutant gene, whereas translation was decreased when EBS1 was overexpressed. The cap binding protein eIF-4E copurifies with Ebs1p in the absence of RNA, suggesting that the two proteins interact in vivo. Although physical and genetic interactions were detected between Ebs1p and Dcp1p, copurification was RNase sensitive, and changes in the expression of Ebs1p had little to no effect on decapping of the MFA2 transcript. The combined results suggest that Ebs1p inhibits translation, most likely through effects on eIF-4E rather than on decapping. Finally, EBS1 transcript levels are under the control of nonsense-mediated mRNA decay (NMD), providing the first example of an NMD-sensitive transcript whose protein product influences a step in gene expression required for NMD.