Up-regulation of RIP1 and IPS-1 in chronic HBV infected patients

IPS-1 and RIP1 are the main downstream molecules of RIG1 and MDA5, as intracytoplasmic receptors, which are the main receptors involved in recognition of internal and external viral double-stranded RNA. In this project, mRNA levels of IPS-1 and RIP1 were investigated in the peripheral blood immune cells of chronic hepatitis B (CHB) patients. IPS-1 and RIP1 mRNA levels were measured in 60 CHB patients and 120 healthy subjects, using RT-qPCR technique. A significant increase in expression levels of IPS-1 and RIP1 was found in patients when compared to healthy individuals. There was no correlation between IPS-1 and RIP1expression levels with the serum levels of hepatitis B e-Antigen (HBeAg) and liver enzymes in patients. Based on the results, it seems that IPS-1 and RIP1 can participate in the induction of low chronic inflammation, which is a main cause of liver cirrhosis and hepatocellular carcinoma.

Assessment of the immunogenicity and protective efficiency of a novel dual-promoter DNA vaccine, harboring SAG1 and GRA7 genes, from RH strain of Toxoplasma gondii in BALB/c mice

BACKGROUND

Toxoplasmosis, a protozoan parasitic disease caused by Toxoplasma gondii, has been a serious human and veterinary medicine problem with global distribution. In the current study, we assessed immunogenicity and protective efficiency of a novel dual-promoter DNA vaccine, harboring SAG1 and GRA7 genes, from RH strain of Toxoplasma gondii (T. gondii) with or without CpG-ODN as adjuvant in a murine model.

METHODS

BALB/c mice were immunized intramuscularly with pVitro-SAG1-GRA7 alone and pVitro-SAG1-GRA7 with CpG-ODN three times at three-week intervals. Enzyme-linked immunosorbent assay (ELISA) was used to assess total IgG, IgG1 and IgG2a antibodies and gamma interferon (IFN-γ) and interleukin-10 (IL-10) cytokines in mice sera. Four weeks post final vaccination, MTT assay and lethal challenge-infection with 1×103 tachyzoites of T. gondii RH strain were carried out to assess stimulation index (SI) and mice survival time, respectively.

RESULTS

The IgG levels in mice immunized with multicomponent vaccines, including pVitro-SAG1-GRA7 alone and pVitro-SAG1-GRA7 with CpG-ODN, were significantly higher than those in control mice or single-gene DNA-vaccinated ones (P<0.05). Furthermore, level of IgG2a in mice receiving pVitro-SAG1-GRA7 with CpG-ODN was significantly higher than that in mice receiving pVitro-SAG1-GRA7 alone (P<0.05). The Toxoplasma lysate antigen (TLA)-stimulated lymphocytes from pVitro-SAG1-GRA7 with CpG-ODN group responded more dramatically than those from control groups or single-gene DNA-vaccinated groups (P<0.001). The pVitro-SAG1-GRA7 with CpG-ODN-vaccinated mice developed high levels of IgG2a and IFN-γ (P<0.001) and low levels of IgG1 and IL-10, compared to control groups, suggesting a modulated immune response type Th1. In addition, survival time of the mice immunized with pVitro-SAG1-GRA7 with CpG-ODN was significantly extended, compared to controls (P<0.05); however, all mice died.

CONCLUSION

The multivalent pVitro-SAG1-GRA7 DNA vaccine with CpG-ODN adjuvant is a promising vaccine candidate against toxoplasmosis.

Engineered zinc-finger nuclease to generate site-directed modification in the KLF1 gene for fetal hemoglobin induction

Elevation of hemoglobin F (HbF) ameliorates symptoms of β-thalassemia, as a common autosomal recessive disorder. In this study, the ability of an engineered zinc-finger nuclease (ZFN) system was assesed to disrupt the KLF1 gene to inhibit the γ to β hemoglobin switching in K562 cells. This study was performed using a second generation integration-deficient lentiviral vector assigned to transient gene targeting. The sequences coding for zinc finger protein arrays were designed and subcloned in TDH plus as a transfer vector. Transduction of K562 cells was performed with the integrase minus lentivirus containing ZFN. The indel percentage of the transducted cells with lentivirus containing ZFN was about 29%. Differentiation of K562 cell line into erythroid cell lineage was induced with cisplatin concentration of 15 µg/mL. After differentiation, γ-globin and HbF expression were evaluated using real-time reverse-transcription polymerase chain reaction and hemoglobin electrophoresis methods. The levels of γ-globin messenger RNA were nine-fold higher in the ZFN treated cells compared with untreated cells 5 days after differentiation. Hemoglobin electrophoresis method showed the same results for HbF level measurement. Application of the ZFN tool to induce KLF1 gene mutation in adult erythroid progenitors might be a candidate to stimulate HbF expression in β-thalassemia patients.

Komagataeibacter xylinus as a novel probiotic candidate with high glucose conversion rate properties

Promoting general health in terms of obesity and diabetes prevention is recommended by health care systems. The objectives of this study were to isolate an efficient glucose-converting Komagataeibacter xylinus to cellulose and to evaluate the safety of the selected strain as a new generation of probiotics in the fight against obesity. Of the 97 samples, 43 K xylinus strains were isolated and evaluated for their glucose conversion rate and 5 strains were examined for probiotic activities by in vitro assays. A strain with significant performance was fed to rats in order to determine its safety status in vivo. The results revealed that the strain K.X.1 had high level of glucose conversion rate and significant survival rate in acidic pH and bile salt. No adverse clinical signs and bacterial translocation to rats’ organs were observed. The results showed that the strain of K. xylinus K.X.1 has suitable probiotic properties.

Circulating free DNA concentration as a marker of disease recurrence and metastatic potential in lung cancer

BACKGROUND

Plasma circulating cell-free (cf) DNA is regarded as a source of tumor DNA. Based on availability of blood tissue for the purposes of early detection of cancer and patients' follow-up, several studies have evaluated concentration of cf DNA in cancer patients in association with tumor features. In the present study, we assessed concentration of cf DNA in lung cancer patients with two commercial kits (MN and QIAGEN) to find whether it can be used as a prognostic biomarker.

RESULTS

Primary cf DNA concentrations as measured by QIAGEN kit was significantly higher in patients who died in the follow-up period compared with alive patients (P = 0.007). Moreover, the concentrations as measured by both methods were higher in patients who experienced recurrence in the follow-up period compared with patients without recurrence (P = 0.008 and 0.007 for MN and QIAGEN kits respectively). Significant associations were also found between cf DNA concentrations and tumor stage (P = 0.005 and 0.02 for MN and QIAGEN kits respectively). Notably, cf DNA concentration was higher in metastatic tumors compared with non-metastatic tumors in association with number of involved organs. Based on the AUC values, both kits could differentiate metastatic cancers from non-metastatic ones with accuracy of 98%.

CONCLUSIONS

The current study highlights the accuracy of cf DNA concentrations for prediction of disease course in lung cancer patients.

Comparison of OmpA Gene-Targeted Real-Time PCR with the Conventional Culture Method for Detection of Acinetobacter baumanii in Pneumonic BALB/c Mice

BACKGROUND

Acinetobacter baumannii is an important pathogen in health care and is responsible for severe nosocomial and community-acquired pneumonia. To design novel therapeutic agents, a mouse model for A. baumannii pneumonia is essential.

METHODS

We described a mouse model of A. baumannii using clinical and 19606R standard strains for developing a quantitative real-time PCR (qRT-PCR) for rapid identification of A. baumannii infection from lung tissues of BALB/c mice.

RESULTS

To infect the mice, three doses of bacteria (0.5 × 108, 1 × 108, and 1.5 × 108 cfu/ml) were used. Lung tissues were cultured and compared with ompA gene. Clinical isolates had better positive results at day three with the highest dose than 19606 strain either in culture (4 versus 3) or in qRT-PCR (5 versus 4). However, qRT-PCR detection was 100%, the specificity was 70%, and the positive predictive value was 27%.

CONCLUSION

The qRT-PCR detection of A. baumannii in the BALB/c mice model has a higher sensitivity than the culture method.

Optimization of chitosan nanoparticles as an anti-HIV siRNA delivery vehicle

Chitosan has emerged as a promising polysaccharide for gene/siRNA delivery. However, additional works will be required to modify chitosan nanoparticles. In the present study, chitosan nanoparticles were well modified to introduce anti-HIV siRNA into two mammalian cell lines, macrophage RAW 264.7 and HEK293. We first generated two stable cell lines expressing HIV-1 Tat, and then designed and generated an efficient anti-tat siRNA. The nanoparticles were prepared by using different concentrations of chitosan, polyethylenimine (PEI) and carboxymethyl dextran (CMD) in various formulations and then their physicochemical and biological properties were investigated. The results demonstrated that the combination of chitosan with both CMD and PEI significantly improved both cell viability and siRNA delivery. The modified chitosan nanoparticles (ChNPs) at the N:P ratio of 50 were approximately uniform spheres with sizes ranging from 100 to 150 nm and a positive zeta potential of about +22 mV. In both cell types, the nanoparticles noticeably increased siRNA delivery efficiency with no significant cytotoxicity or apoptosis-inducing effects compared to the control cells. In addition, the nanoparticles significantly reduced the RNA and protein expression of HIV-1 tat in both stable cells. These data show that the nanoparticle formulation could potentially be used in gene therapy, especially against HIV infection.

Evaluation of Novel Probiotic Bacillus Strains Based on Enzyme Production and Protective Activity Against Salmonellosis

Probiotic strains of Bacillus Species are used in industrial poultry production because of their ability to produce enzymes enhancing the absorption of food, and their ability to reduce the risk of Salmonella spp. infection. The aim of this study was to isolate native potential probiotic Bacillus spp. with the ability to produce enzymes and attachment to intestinal epithelial cells in order to prevent Salmonella typhimurium infection. First, 25 samples of chicken feces were collected from 7 industrial poultry in Golestan province located in north of Iran. Bacillus species from samples were isolated on nutrient agar. These strains were evaluated for the ability of producing amyalse and phytase and their probiotic characteristics such as bile salt, acid and antibiotic resistance, the ability to attach to intestinal epithelial cells and inhibit Salmonella typhimurium invasion. Then selected isolates were identified based on 16S rDNA.  Results showed that from 86 isolated, 4 Bacillus strains‌ had desirable characteristics such as the ability to produce phytase and amylase and having suitable probiotics features. We identified K03, K02, and K20 isolates as Bacillus tequilensis and K20 as Bacillus subtilis. Bacillus tequilensis K03 showed the highest attachment ability to intestinal epithelium cells and could inhibited Salmonella typhimurium attachment.

You are what you eat: Sequence analysis reveals how plant microRNAs may regulate the human genome

BACKGROUND

Nutrigenomic has revolutionized our understanding of nutrition. As plants make up a noticeable part of our diet, in the present study we chose microRNAs of edible plants and investigated if they can perfectly match human genes, indicating potential regulatory functionalities.

METHODS

miRNAs were obtained using the PNRD database. Edible plants were separated and microRNAs in common in at least four of them entered our analysis. Using vmatchPattern, these 64 miRNAs went through four steps of refinement to improve target prediction: Alignment with the whole genome (2581 results), filtered for those in gene regions (1371 results), filtered for exon regions (66 results) and finally alignment with the human CDS (41 results). The identified genes were further analyzed in-silico to find their functions and relations to human diseases.

RESULTS

Four common plant miRNAs were identified to match perfectly with 22 human transcripts. The identified target genes were involved in a broad range of body functions, from muscle contraction to tumor suppression. We could also indicate some connections between these findings and folk herbology and botanical medicine.

CONCLUSIONS

The food that we regularly eat has a great potential in affecting our genome and altering body functions. Plant miRNAs can provide means of designing drugs for a vast range of health problems including obesity and cancer, since they target genes involved in cell cycle (CCNC), digestion (GIPR) and muscular contractions (MYLK). They can also target regions of CDS for which we still have no sufficient information, to help boost our knowledge of the human genome.

Construction of a chimeric antigen receptor bearing a nanobody against prostate a specific membrane antigen in prostate cancer

Adoptive transfer of T cells expressing chimeric antigen receptors (CARs) is considered to be a novel anticancer therapy. To date, in most cases, single-chain variable fragments (scFvs) of murine origin have been used in CARs. However, this structure has limitations relating to the potential immunogenicity of mouse antigens in humans and the relatively large size of scFvs. For the first time, we used camelid nanobody (VHH) to construct CAR T cells against prostate specific membrane antigen (PSMA). The nanobody against PSMA (NBP) was used to show the feasibility of CAR T cells against prostate cancer cells. T cells were transfected, and then the surface expression of the CAR T cells was confirmed. Then, the functions of VHH-CAR T cell were evaluated upon coculture with prostate cancer cells. At the end, the cytotoxicity potential of NBPII-CAR in T cells was approximated by determining the cell surface expression of CD107a after encountering PSMA. Our data show the specificity of VHH-CAR T cells against PSMA⁺ cells (LNCaP), not only by increasing the interleukin 2 (IL-2) cytokine (about 400 pg/mL), but also the expression of CD69 by almost 38%. In addition, VHH-CAR T cells were proliferated by nearly 60% when cocultured with LNCaP, as compared with PSMA negative prostate cancer cell (DU-145), which led to the upregulation of CD107a in T cells upto 31%. These results clearly show the possibility of using VHH-based CAR T cells for targeted immunotherapy, which may be developed to target virtually any tumor-associated antigen for adoptive T-cell immunotherapy of solid tumors.

Obtaining and characterization of anti-testis monoclonal antibodies: Invaluable tools toward the identification of testis antigens involved in fertilization

BACKGROUND

Generation and utilization of the specific monoclonal antibodies against testis antigens is reported to identify the antigens that are important in reproductive field.

OBJECTIVE

Current study aimed to introduce a hybridoma that producing a specific anti-testis monoclonal antibody to identify the testis antigens that can be important in the reproduction field.

METHODS

To make hybridoma against testis antigens, mice were immunized with testis cell lysate. After cell fusion, resulted hybridomas were screened by indirect ELISA, then cloned by limiting dilution and finally the produced monoclonal antibody were characterized by some of the molecular laboratory techniques such as immunohistochemistry, immunocytochemistry and western blot.

RESULTS

By using hybridoma technique, cell fusion was performed and ten (8A11, 8D6, 8D7, 9F6, 9G11, 10C3, 10B3, 10B2, 10C2 and 10H7) antibodies specific to the testis antigens were produced finally. Among the produced antibodies, 10C3 was found to cross-react with testis, but not detected in other tissues. mAb 10C3 recognized the sperm and testis antigens, specifically the intertestitial tissue of testis, spermatogonia, primary and secondary spermatocyte antigens, so they were most likely the target of generated mAb. Also our mAb could totally detect the mouse sperm antigens and the specific antigens of head and tail of human sperm. In western blotting analysis, mAb 10C3 could recognize the specific protein bands of sperm and testis extracts. Also in this study the testis specific genes that were target of generated mAb, were selected according to the mouse EST profile available at UniGene part of NCBI.

CONCLUSIONS

So this stable anti-testis mAb has a potential for laboratory researches and also for diagnostic procedures in fertilization. Thus it could be exploited as a suitable tool for target-specific diagnosis and research in several diseases.

Expression profile of miRNAs in urine samples of bladder cancer patients

AIM

miRNAs have been suggested as biomarkers for bladder cancer. We aimed to find a diagnostic panel of miRNAs based on differential expression of miRNAs in urine specimens of patient with bladder cancer compared with control group.

METHODS

miR-141, miR-10b, miR-34b and miR-103 were selected to assess their expression in urine samples of 66 bladder cancer patients and 53 matched controls using quantitative real time PCR.

RESULTS

miR-10b and miR-34b were upregulated in cases compared with controls. The combination of four miRNAs showed a sensitivity of 75% and specificity of 63.5% with a diagnostic power of 72%.

CONCLUSION

Certain miRNAs can be used as biomarkers for early diagnosis of bladder cancer.

Urinary exosomal expression of long non-coding RNAs as diagnostic marker in bladder cancer

Background

Long non-coding RNAs (lncRNAs) and exosomes have been regarded as components of cell signal transmission that modulate indigenous cellular microenvironments. Exosomes also participate in relocation of functional lncRNAs between cells.

Methods

In the present study, we evaluated expression of LINC00355, LINC00958, UCA1-201, UCA1-203, and MALAT1 lncRNAs in urinary exosomes isolated from transitional cell carcinoma (TCC) of bladder, non-malignant urinary disorders, and normal subjects.

Results

LINC00355, UCA1-203, and MALAT1 expression was significantly higher in TCC patients compared to controls (non-malignant or normal samples). However, UCA1-201 expression was significantly decreased in TCC patients compared with controls. LINC00355 and MALAT1 expression was significantly lower in cigarette smokers and opium-addicted TCC patients, respectively. On the other hand, LINC00355 expression tended to be higher in opium-addicted TCC patients. The proposed panel of lncRNAs (composed of UCA1-201, UCA1-203, MALAT1, and LINC00355) had 92% sensitivity and 91.7% specificity for diagnosis of bladder cancer from normal samples.

Conclusion

Transcript levels of lncRNAs in urinary exosomes are potential diagnostic bio-markers in bladder cancer.

Applying simple linear combination, multiple logistic and factor analysis methods for candidate fecal bacteria as novel biomarkers for early detection of adenomatous polyps and colon cancer

BACKGROUND

Colorectal cancer (CRC) is the third leading cause of cancer, and presents a considerable disease burden, worldwide. Recently, the gut microbiota has been proposed as a potential risk factor for CRC, and even adenomatous polyps (AP). Here, the aim of this study was to investigate the role of selected gut bacteria as fecal bacterial biomarkers, in early detection of CRC and AP.

MATERIAL AND METHODS

Fecal samples (n = 93) were collected from Taleghani Hospital, Tehran, Iran, between 2015 and 2017, from normal controls (NC), AP cases and CRC stage I patients, who were undergoing screening for colonoscopy. Absolute quantitative real time PCR (qPCR) assays were established for the quantification of bacterial marker candidates, in all cases and control groups. In order to evaluate the diagnostic value of bacterial candidates in distinguishing CRC from a polyp, receiver operating characteristic curve (ROC) was performed. Multiple logistic regressions were used to find the best combinations of the bacterial candidates, then, combinations were analyzed based on three methods, including linear combination, multiple logistic and factor analysis models.

RESULTS

According to the logistic model, combination of Fusobacterium nucleatum, Enterococcus feacalis, Streptococcus bovis, Enterotoxigenic Bacteroides fragilis (ETBF) and Porphyromonas spp. showed improved diagnostic performance, compared to each bacterium alone, as area under the receiver operating characteristic (AUROC) increases to 0.97, with 95% confidence interval. It was found that a simple linear combination was an appropriate model for discriminating AP and CRC cases, compared to the NC, with a sensitivity of 91.4% and specificity of 93.5%.

CONCLUSION

Our results indicated that based on fecal bacterial candidates, statistical simple linear combination model and ROC curve analysis, early detection of AP and CRC might be possible.

Urine exosome gene expression of cancer-testis antigens for prediction of bladder carcinoma

Background

Exosomes have been regarded as emerging tools for cancer diagnosis. Tumor-derived exosomes contain molecules that enhance cancer progression and affect immune responses.

Material and methods

In the present study, we evaluated expression of seven cancer-testis antigens (CTAs) that are regarded as putative biomarkers and immunotherapeutic targets along with NMP22 in urinary exosomes of bladder cancer patients, healthy subjects and patients affected with nonmalignant urinary disorders.

Results

Exosomal expression of MAGE-B4 was significantly higher in bladder cancer patients compared with normal samples (expression ratio=2.68, P=0.01). However, its expression was lower in bladder cancer patients compared with benign prostate hyperplasia (BPH) patients (expression ratio=0.17, P=0.01). Exosomal expression of NMP22 was significantly higher in bladder cancer patients compared with BPH patients (expression ratio=9.22, P=0.02). Expressions of other genes were not significantly different between bladder cancer patients and normal/nonmalignant samples. We found significant correlation between MAGE-A3 and MAGE-B4 expressions in exosomes obtained from controls. In addition, TSGA10 expression was correlated with expression of NMP22 in both cancer patients and controls.

Conclusion

The present study provides evidences for differential expression of CTAs in urinary exosomes of bladder cancer patients and urogenital disorders and warrants further studies for assessment of their significance in cancer diagnosis and immunotherapeutic approaches.

Investigating Association of rs5918 Human Platelets Antigen 1 and rs1800790 Fibrinogen β Chain as Critical Players with Recurrent Pregnancy Loss

Thrombophilia gene variants have been shown to be associated with higher risk of recurrent pregnancy loss (RPL). Due to the role of human platelets antigen 1 (HPA-1) and fibrinogen β chain (FGB) as critical players in the coagulation process, their most important variants including rs5918 T > C and rs1800790 G > A were selected to be studied in women affected by RPL. Three milliliters of peripheral blood were drawn from 110 women with history of at least two consecutive spontaneous abortion and 110 healthy women controls. rs5918 T > C and rs1800790 G > A of HPA-1 and FGB genes, respectively, were selected to be analyzed through polymerase chain reaction-restriction fragment length polymorphism (PCR_RFLP) following DNA isolation using QIAamp DNA Blood Mini Kit. Heterozygote genotype (TC) of HPA-1 gene rs5918 polymorphism was significantly associated with risk of RPL (p-value = 0.02). Although, rs1800790 G > A of FGB gene was not associated with RPL, its combination with rs5918 polymorphism was associated with increased risk of RPL. Owing to the critical roles of FGB and HPA-1 genes in coagulation, and thrombosis and several confinements on the meaningful association between the combination of those polymorphism with risk of RPL, including them in the thrombophilia panel may increase detection rate of hereditary thrombophilia patients. However, further studies with larger sample sizes are required to shed light on the exact role of the studied gene polymorphism, especially rs1800790 G > A of FGB gene variant in pathogenesis of RPL.

A potential clinical significance of DAB2IP and SPRY2 transcript variants in prostate cancer

Deregulation of key signaling pathways is one of the primary phenomena in carcinogenesis. DAB2IP and SPRY2 are regulatory elements, which act as feedback inhibitors of receptor tyrosine kinases signaling in mitogen-activated protein kinase pathway. These elements have also been implicated in the pathophysiology of cancer. Therefore, this study is aimed to investigate the expression of all known splice variants of DAB2IP and SPRY2 in prostate tissue. Fresh Prostate tissue samples (50 prostate cancer/ matched normal tissue and 30 BPH) were collected and total RNA was extracted followed by cDNA synthesis. The expression of DAB2IP and SPRY2 transcript variants were evaluated using RT-PCR and quantitative Real-time PCR. The results indicated significant down-regulation of DAB2IP transcript variant 1 in cancerous tissues compared to paired normal tissues (P = 0.001) as well as SPRY2 transcript variant 2 in cancerous tissues in comparison with the normal counterparts and BPH (P = 0.008 and P = 0.025, respectively). In addition, there was a significant negative correlation between DAB2IP.1 and SPRY2.2 expression with PSA levels in prostate cancer (P = 0.039 ρ =-0.24 and P = 0.045 ρ =-0.3, respectively). Interestingly, the down-regulation of DAB2IP.1 mRNA and SPRY2.2 mRNA was positively correlated in tumor samples (P = 0.002 ρ = 0.434). For the first time, this experiment highlights the deregulation of DAB2IP and SPRY2 transcript variants in human prostate cancer. The present study confirms and extends the previous reports through indicating transcript-specific down-regulation and significant association of DAB2IP and SPRY2 in prostate tumorigenesis.

Combining Supervised and Unsupervised Learning for Improved miRNA Target Prediction

MicroRNAs (miRNAs) are short non-coding RNAs which bind to mRNAs and regulate their expression. MiRNAs have been found to be associated with initiation and progression of many complex diseases. Investigating miRNAs and their targets can thus help develop new therapies by designing anti-miRNA oligonucleotides. While existing computational approaches can predict miRNA targets, these predictions have low accuracy. In this paper, we propose a two-step approach to refine the results of sequence-based prediction algorithms. The first step, which is based on our previous work, uses an ensemble learning approach that combines multiple existing methods. The second step utilizes support vector machine (SVM) classifiers in one- and two-class modes to infer miRNA-mRNA interactions based on both binding features, as well as network features extracted from gene regulatory network. Experimental results using two real data sets from TCGA indicate that the use of two-class SVM classification significantly improves the precision of miRNA-mRNA prediction.