Immunogenicity and protective efficacy of orally administered recombinant Lactobacillus plantarum expressing VP2 protein against IBDV in chicken

AIM

To develop an effective oral vaccine against the very virulent infectious bursal disease virus (vvIBDV), we generated two recombinant Lactobacillus plantarum strains (pPG612-VP2/LP and pPG612-T7g10-VP2/LP, which carried the T7g10 translational enhancer) that displayed the VP2 protein on the surface, and compared the humoral and cellular immune responses against vvIBDV in chickens.

METHODS AND RESULTS

We genetically engineered the L. plantarum strains pPG612-VP2/LP and pPG612-T7g10-VP2/LP constitutively expressing the VP2 protein of vvIBDV. We found that the T7g10 enhancer efficiently upregulates VP2 expression in pPG612-T7g10-VP2/LP. Orally administered, pPG612-T7g10-VP2/LP exhibited significant levels of protection (87·5%) against vvIBDV in chickens, indicating improved immunogenicity. Chickens in the pPG612-T7g10-VP2/LP group produced higher levels of interferons (IFN-γ) and interleukins (IL-2 and IL-4) than those in the pPG612-VP2/LP group. CD8+ and CD4+ lymphocyte counts indicated greater stimulation in the pPG612-T7g10-VP2/LP group (13·3 and 21·0% respectively) than in the pPG612-VP2/LP group (10·4 and 14·0% respectively). Thus, pPG612-T7g10-VP2/LP could induce strong humoral and cellular immune responses against vvIBDV.

CONCLUSIONS

The recombinant L. plantarum that expresses pPG612-T7g10-VP2 is a promising candidate for oral vaccine development against vvIBDV.

SIGNIFICANCE AND IMPACT OF THE STUDY

The recombinant Lactobacillus delivery system provides a promising strategy for vaccine development against vvIBDV in chickens.

Metabolomic identification of diagnostic serum-based biomarkers for advanced stage melanoma

INTRODUCTION

Melanoma is a highly aggressive malignancy and is currently one of the fastest growing cancers worldwide. While early stage (I and II) disease is highly curable with excellent prognosis, mortality rates rise dramatically after distant spread. We sought to identify differences in the metabolome of melanoma patients to further elucidate the pathophysiology of melanoma and identify potential biomarkers to aid in earlier detection of recurrence.

METHODS

Using ¹H NMR and DI-LC-MS/MS, we profiled serum samples from 26 patients with stage III (nodal metastasis) or stage IV (distant metastasis) melanoma and compared their biochemical profiles with 46 age- and gender-matched controls.

RESULTS

We accurately quantified 181 metabolites in serum using a combination of ¹H NMR and DI-LC-MS/MS. We observed significant separation between cases and controls in the PLS-DA scores plot (permutation test p-value = 0.002). Using the concentrations of PC-aa-C40:3, DL-carnitine, octanoyl-L-carnitine, ethanol, and methylmalonyl-L-carnitine we developed a diagnostic algorithm with an AUC (95% CI) = 0.822 (0.665-0.979) with sensitivity and specificity of 100 and 56%, respectively. Furthermore, we identified arginine, proline, tryptophan, glutamine, glutamate, glutathione and ornithine metabolism to be significantly perturbed due to disease (p < 0.05).

CONCLUSION

Targeted metabolomic analysis demonstrated significant differences in metabolic profiles of advanced stage (III and IV) melanoma patients as compared to controls. These differences may represent a potential avenue for the development of multi-marker serum-based assays for earlier detection of recurrences, allow for newer, more effective targeted therapy when tumor burden is less, and further elucidate the pathophysiologic changes that occur in melanoma.

Senescence mirrors the extent of liver fibrosis in chronic hepatitis C virus infection

BACKGROUND

Chronic viral hepatitis is linked to fibrotic liver injury that can progress to liver cirrhosis with its associated complications. Recent evidence suggests a role of senescence in liver fibrosis, although the senescence regulators contributing to fibrosis progression remain unclear.

AIM

To investigate the role of senescence and different senescence markers for fibrosis progression in patients with chronic hepatitis C virus (HCV) infection.

METHODS

The expression of the cell cycle inhibitors p21, p27 and p16 as well as the senescence markers p-HP1γ and γ-H2AX was analysed in liver tissue with different fibrosis stages. Senescence-associated chitotriosidase activity was measured in sera of HCV patients (n = 61) and age-matched healthy individuals (n = 22).

RESULTS

We found a remarkable up-regulation of the cell cycle inhibitors and senescence markers in chronic HCV infection compared to healthy liver tissue. Liver tissue with relevant fibrosis stages (F2-3) or cirrhosis (F4) revealed a significant increase in senescent cells compared to livers with no or minimal fibrosis (F0-1). In cirrhotic livers, a significantly higher number of p-HP1γ, p21 and p27 positive cells was detected compared to liver tissue with F2-3 fibrosis. Importantly, we identified T-cells as the dominant cell type contributing to increased senescence during fibrosis progression. Compared to healthy individuals, serum chitotriosidase was significantly elevated and correlated with histological fibrosis stages and liver stiffness as assessed by transient elastography.

CONCLUSIONS

Senescence of hepatic T-cells is enhanced in chronic viral hepatitis and increases with fibrosis progression. Serological detection of senescence-associated chitotriosidase might allow for the non-invasive detection of relevant fibrosis stages.

Research on the correlation between the polymorphism of the back-2 gene and osteoarthritis

OBJECTIVE

The objective of the present study was to investigate the correlation between polymorphisms of the back-2 gene and osteoarthritis.

PATIENTS AND METHODS

We enrolled 76 patients with osteoarthritis who were admitted to our hospital between February 2014 and February 2015 for treatment as the observation group, and 46 healthy subjects as the control group. The analysis of back-2 gene polymorphisms (rs28502) was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). mRNA expression of the different genotypes was measured with reverse transcriptase-polymerase chain reaction (RT-PCR), and the protein expression of back-2 of different genotypes was measured with enzyme-linked immunosorbent assay (ELISA) and Western blotting.

RESULTS

At locus 173 of the back-2 gene, there were a total of three genotypes, i.e. CC, CT, and TT. The frequencies of these genotypes in healthy subjects and osteoarthritis patients were 9.5%, 82.2%, 8.3% and 47.4%, 7.5%, 45.1%, respectively. There was a significant difference (p<0.05). However, the frequency of C/T in healthy older subjects and osteoarthritis patients was 50.6%, 49.4%, 51.15%, 48.85%, respectively, and there was no significant difference (p>0.05). RT-PCR showed no significant difference in mRNA expressions of the back-2 gene between the control group and observation group (p>0.05), although ELISA indicated that the protein expression of back-2 (12.3±0.36 μg/L) in osteoarthritis patients was significantly higher than in healthy subjects (1.52±0.18 μg/L) (p<0.05). Moreover, Western blotting analysis indicated that the protein expression of back-2 in osteoarthritis patients was significantly higher than in healthy subjects.

CONCLUSIONS

Genetic polymorphisms of back-2 are associated with the metabolic syndrome in older people, i.e. older people with the CC or TT genotypes may be at high risk for metabolic syndrome.

Production of photoionized plasmas in the laboratory with x-ray line radiation

In this paper we report the experimental implementation of a theoretically proposed technique for creating a photoionized plasma in the laboratory using x-ray line radiation. Using a Sn laser plasma to irradiate an Ar gas target, the photoionization parameter, ξ=4πF/N_{e}, reached values of order 50ergcms^{-1}, where F is the radiation flux in ergcm^{-2}s^{-1}. The significance of this is that this technique allows us to mimic effective spectral radiation temperatures in excess of 1 keV. We show that our plasma starts to be collisionally dominated before the peak of the x-ray drive. However, the technique is extendable to higher-energy laser systems to create plasmas with parameters relevant to benchmarking codes used to model astrophysical objects.

Increasing the power of meta-analysis of genome-wide association studies to detect heterogeneous effects

Motivation

Meta-analysis is essential to combine the results of genome-wide association studies (GWASs). Recent large-scale meta-analyses have combined studies of different ethnicities, environments and even studies of different related phenotypes. These differences between studies can manifest as effect size heterogeneity. We previously developed a modified random effects model (RE2) that can achieve higher power to detect heterogeneous effects than the commonly used fixed effects model (FE). However, RE2 cannot perform meta-analysis of correlated statistics, which are found in recent research designs, and the identified variants often overlap with those found by FE.

Results

Here, we propose RE2C, which increases the power of RE2 in two ways. First, we generalized the likelihood model to account for correlations of statistics to achieve optimal power, using an optimization technique based on spectral decomposition for efficient parameter estimation. Second, we designed a novel statistic to focus on the heterogeneous effects that FE cannot detect, thereby, increasing the power to identify new associations. We developed an efficient and accurate p-value approximation procedure using analytical decomposition of the statistic. In simulations, RE2C achieved a dramatic increase in power compared with the decoupling approach (71% vs. 21%) when the statistics were correlated. Even when the statistics are uncorrelated, RE2C achieves a modest increase in power. Applications to real genetic data supported the utility of RE2C. RE2C is highly efficient and can meta-analyze one hundred GWASs in one day.

Availability and implementation

The software is freely available at http://software.buhmhan.com/RE2C.

Supplementary information

Supplementary data are available at Bioinformatics online.

Genetic association of the ACACB gene with milk yield and composition traits in dairy cattle

Previously, we re-sequenced the whole genomes of eight Holstein bulls with high or low milk protein and fat percentage, and we detected two indels in the ACACB (acetyl-CoA carboxylase beta) gene that were polymorphic between the two groups. Thus, we considered ACACB as a promising candidate gene potentially affecting milk composition traits. Herein, we verified the genetic effects of ACACB on five milk traits in a Chinese Holstein population. We identified six SNPs in the 5'-promoter region, five in the 5'- untranslated region (UTR), 11 in exons, four in the 3'-UTR and three in the 3'-flanking region by re-sequencing the entire coding and regulatory regions of ACACB. One of these SNPs (ss1987461005) is reported here for the first time, and three of the SNPs (rs109482081, rs110819816 and rs109281947) were predicted to result in amino acid replacements. Genotype-phenotype association analyses showed that all the identified SNPs, except for ss1987461005, rs208919019 and rs134447911, were significantly associated with milk yield, fat yield, fat percentage, protein yield or protein percentage (P < 0.0001 to 0.0484). Linkage disequilibrium analyses were conducted among the identified SNPs to confirm the genetic associations. Two SNPs-rs135874354 (g.66218726T>C) and rs210928430 (g.66218117G>A)-were predicted to alter transcription factor binding sites in the 5'-promoter region of ACACB. A luciferase activity assay showed that the promoter activity of haplotype TG was significantly higher than that of CG (P = 0.0002) and that the promoter activity of haplotype TA was remarkably higher than that of CA (P = 7.4285E-09), showing that the T allele of rs135874354 increased promoter activity. Thus, rs135874354 was considered to be a potentially functional mutation. Our findings have, for the first time, profiled the genetic effect of ACACB on milk production traits in dairy cattle and revealed a potentially causal mutation that requires further the in-depth validation.

Resistance characterization of ledipasvir and velpatasvir in hepatitis C virus genotype 4

HCV genotype 4 (GT4) has often been overlooked in drug development, even though it infects ~20 million people worldwide. Ledipasvir/sofosbuvir and sofosbuvir/velpatasvir were highly efficacious in GT4 HCV-infected patients from GS-US-337-1119 and GS-US-342-1138. Here, we characterize the resistance profile of ledipasvir (LDV) and velpatasvir (VEL) in patients with GT4 HCV infection. NS5A deep-sequencing was performed for 454 patients infected with HCV GT4 at baseline, including 44 patients enrolled in GS-US-337-1119 and 116 patients enrolled in GS-US-342-1138, and at relapse for patients with virologic failure. LDV and VEL susceptibilities of 56 patient isolates were determined. In GS-US-337-1119, SVR12 rates were 100% for all subtypes except 4b and 4r. Phenotypic assessment of 56 HCV NS5A patient isolates from various GT4 subtypes indicated that LDV had high potency for the common subtypes 4a/d, and subtypes 4c/f/k/l/m/n/o/p/r/t despite the presence of resistance-associated substitutions (RASs). For the rare GT4b, LDV median EC₅₀ was higher, but with a broad range of individual values. Importantly, all GT4b isolates tested had 2-4 NS5A RASs, some including Y93H. Similarly, the 2 GT4r infected patients who had virologic relapse had rare triple RASs. Reversion of these substitutions to the consensus residue significantly increased LDV susceptibility. In GS-US-342-1138, all patients achieved SVR12, regardless of their subtype or presence of RASs. In vitro data confirmed that VEL is potent against all GT4 isolates tested. LDV and VEL are potent antiviral drugs, estimated to be effective against >95% and >99%, respectively, of GT4 HCV isolates.

Genetic variations in cancer-related significantly mutated genes and lung cancer susceptibility

Background

Cancer initiation and development are driven by key mutations in driver genes. Applying high-throughput sequencing technologies and bioinformatic analyses, The Cancer Genome Atlas (TCGA) project has identified panels of somatic mutations that contributed to the etiology of various cancers. However, there are few studies investigating the germline genetic variations in these significantly mutated genes (SMGs) and lung cancer susceptibility.

Patients and methods

We comprehensively evaluated 1655 tagged single nucleotide polymorphisms (SNPs) located in 127 SMGs identified by TCGA, and test their association with lung cancer risk in large-scale case-control study. Functional effect of the validated SNPs, gene mutation frequency and pathways were analyzed.

Results

We found 11 SNPs in 8 genes showed consistent association (P < 0.1) and 8 SNPs significantly associated with lung cancer risk (P < 0.05) in both discovery and validation phases. The most significant association was rs10412613 in PPP2R1A, with the minor G allele associated with a decreased risk of lung cancer [odds ratio = 0.91, 95% confidence interval (CI): 0.87-0.96, P = 2.3 × 10-4]. Cumulative analysis of risk score built as a weight sum of the 11 SNPs showed consistently elevated risk with increasing risk score (P for trend = 9.5 × 10-9). In stratified analyses, the association of PPP2R1A:rs10412613 and lung cancer risk appeared stronger among population of younger age at diagnosis and never smokers. The expression quantitative trait loci analysis indicated that rs10412613, rs10804682, rs635469 and rs6742399 genotypes significantly correlated with the expression of PPP2R1A, ATR, SETBP1 and ERBB4, respectively. From TCGA data, expression of the identified genes was significantly different in lung tumors compared with normal tissues, and the genes' highest mutation frequency was found in lung cancers. Integrative pathway analysis indicated the identified genes were mainly involved in AKT/NF-κB regulatory pathway suggesting the underlying biological processes.

Conclusion

This study revealed novel genetic variants in SMGs associated with lung cancer risk, which might contribute to elucidating the biological network involved in lung cancer development.

Risk factors for biopsy-proven advanced non-alcoholic fatty liver disease in the Veterans Health Administration

BACKGROUND

With its increasing incidence, nonalcoholic fatty liver disease (NAFLD) is of particular concern in the Veterans Health Administration (VHA).

AIMS

To evaluate risk factors for advanced fibrosis in biopsy-proven NAFLD in the VHA, to identify patients at risk for adverse outcomes.

METHODS

In randomly selected cases from VHA databases (2005-2015), we performed a retrospective case-control study in adults with biopsy-defined NAFLD or normal liver.

RESULTS

Of 2091 patients reviewed, 399 met inclusion criteria. Normal controls (n = 65) had normal liver function. The four NAFLD cohorts included: NAFL steatosis (n = 76), nonalcoholic steatohepatitis (NASH) without fibrosis (n = 68), NAFLD/NASH stage 1-3 fibrosis (n = 82), and NAFLD/NASH cirrhosis (n = 70). NAFLD with hepatocellular carcinoma (HCC) was separately identified (n = 38). Most patients were older White men. NAFLD patients with any fibrosis were on average severely obese (BMI>35 kg/m² ). Diabetes (54.4%-79.6%) and hypertension (85.8%-100%) were more common in NAFLD with fibrosis or HCC. Across NAFLD, 12.3%-19.5% were enrolled in diet/exercise programs and 0%-2.6% had bariatric surgery. Hispanics exhibited higher rates of NASH (20.6%), while Blacks had low NAFLD rates (1.4%-11.8%), particularly NAFLD cirrhosis and HCC (1.4%-2.6%). Diabetes (OR 11.8, P < .001) and BMI (OR 1.4, P < .001) were the most significant predictors of advanced fibrosis.

CONCLUSIONS

In the VHA, diabetes and severe obesity increased risk for advanced fibrosis in NAFLD. Of these patients, only a small proportion (~20%) had enrolled in diet/exercise programs or had bariatric surgery (~2%). These results suggest that providers should focus/tailor interventions to improve outcomes, particularly in those with diabetes and severe obesity.

Bevacizumab and gefitinib enhanced whole-brain radiation therapy for brain metastases due to non-small-cell lung cancer

Non-small-cell lung cancer (NSCLC) patients who experience brain metastases are usually associated with poor prognostic outcomes. This retrospective study proposed to assess whether bevacizumab or gefitinib can be used to improve the effectiveness of whole brain radiotherapy (WBRT) in managing patients with brain metastases. A total of 218 NSCLC patients with multiple brain metastases were retrospectively included in this study and were randomly allocated to bevacizumab-gefitinib-WBRT group (n=76), gefitinib-WBRT group (n=77) and WBRT group (n=75). Then, tumor responses were evaluated every 2 months based on Response Evaluation Criteria in Solid Tumors version 1.0. Karnofsky performance status and neurologic examination were documented every 6 months after the treatment. Compared to the standard WBRT, bevacizumab and gefitinib could significantly enhance response rate (RR) and disease control rate (DCR) of WBRT (P<0.001). At the same time, RR and DCR of patients who received bevacizumab-gefitinib-WBRT were higher than those who received gefitinib-WBRT. The overall survival (OS) rates and progression-free survival (PFS) rates also differed significantly among the bevacizumab-gefitinib-WBRT (48.6 and 29.8%), gefitinib-WBRT (36.7 and 29.6%) and WBRT (9.8 and 14.6%) groups (P<0.05). Although bevacizumab-gefitinib-WBRT was slightly more toxic than gefitinib-WBRT, the toxicity was tolerable. As suggested by prolonged PFS and OS status, bevacizumab substantially improved the overall efficacy of WBRT in the management of patients with NSCLC.

Identification of the novel allele, HLA-B*15:388, in a Chinese bone marrow donor

The novel allele, HLA-B*15:388, was identified in a Chinese bone marrow donor by sequence-based typing.

Atom probe tomographic assessment of the distribution of germanium atoms implanted in a silicon matrix through nano-apertures

Ion implantation through nanometer-scale apertures (nano-apertures) is a promising method to precisely position ions in silicon matrices, which is a requirement for next generation electronic and quantum computing devices. This paper reports the application of atom probe tomography (APT) to investigate the three-dimensional distribution of germanium atoms in silicon after implantation through nano-aperture of 10 nm in diameter, for evaluation of the amount and spatial distribution of implanted dopants. The experimental results obtained by APT are consistent with a simple simulation with consideration of several effects during lithography and ion implantation, such as channeling and resist flow.

LSD1 demethylates HIF1α to inhibit hydroxylation and ubiquitin-mediated degradation in tumor angiogenesis

Lysine-specific demethylase 1 (LSD1), which has been considered as a potential therapeutic target in human cancer, has been known to regulate many biological functions through its non-histone substrates. Although LSD1-induced hypoxia-inducible factor alpha (HIF1α) demethylation has recently been proposed, the effect of LSD1 on the relationship between HIF1α post-translational modifications (PTMs) and HIF1α-induced tumor angiogenesis remains to be elucidated. Here, we identify a new methylation site of the HIF1α protein antagonized by LSD1 and the interplay between HIF1α protein methylation and other PTMs in regulating tumor angiogenesis. LSD1 demethylates HIF1α at lysine (K) 391, which protects HIF1α against ubiquitin-mediated protein degradation. LSD1 also directly suppresses PHD2-induced HIF1α hydroxylation, which has a mutually dependent interplay with Set9-mediated HIF1α methylation. Moreover, the HIF1α acetylation that occurs in a HIF1α methylation-dependent manner is inhibited by the LSD1/NuRD complex. HIF1α stabilized by LSD1 cooperates with CBP and MTA1 to enhance vascular endothelial growth factor (VEGF)-induced tumor angiogenesis. Thus, LSD1 is a key regulator of HIF1α/VEGF-mediated tumor angiogenesis by antagonizing the crosstalk between PTMs involving HIF1α protein degradation.