The non-structural 5B (NS5B) gene is the target region to identify hepatitis C virus (HCV) subtypes. However, it is not always possible to amplify this region because of inherently high sequence variability. Nucleotide sequences of the non-structural 5A (NS5A) and NS5B genes and its concordance were determined from patients infected with HCV genotype 1 (HCV-1). Among the 30 HCV-1 samples, 7 (23%) were identified as subtype 1a and 23 (77%) were identified as 1b by NS5A sequencing. Sequence analysis of the NS5B showed that 13 (43%) were identified as 1a and 17 (57%) were identified as 1b. Out of the 13 samples identified as 1a by NS5B, 6 (46%) were correctly identified by NS5A. Of the 17 samples identified as 1b by NS5B, 16 (94%) were correctly identified by NS5A. The presence of glutamic acid (E) or aspartic acid (D) at position 2225 in the NS5A differentiates 1a from 1b subtypes, respectively. This study showed that the NS5A sequencing can identify HCV-1a and 1b subtypes with predictive values of 86% and 70% of cases, respectively. The overall concordance with NS5B was 73%. NS5B sequence analysis remains to be the reference method to identify HCV-1 subtypes. NS5A sequencing may be used to complement NS5B sequencing in case the NS5B gene cannot be successfully amplified.

Human ; Male ; Female ; Aged ; Middle Aged ; Adult ; ; Aspartic Acid ; Genotype ; Glutamic Acid ; Hepacivirus ; Hepatitis C ; Nucleotides ; Sequence Analysis ; Viral Nonstructural Proteins

INTRODUCTION: Urinary proteomics provides a wealth of information in the identification of protein markers associated with various diseases such as in carcinoma. With the increasing incidence of prostate cancer and the lack of sensitivity and specificity of prostate specific antigen, the simultaneous identification of an alternative protein biomarker through urinary proteomics is encouraging. Urine, which has similar proteins with serum, makes it an ideal alternative biofluid wherein the collection is easy and non-invasive.
METHODS: Urinary proteins were separated by gradient SDS-PAGE followed by in-gel digestion and organic/buffer peptide extraction. The protein biomarkers in prostate cancer patients and control subjects were identified via LC-MS/MS and submitted to Protein Prospector where the peptide fragmentation of sequence was analyzed and compared with the SwissProt database.
RESULTS: A panel of three protein biomarkers for the early detection of prostate cancer were identified: transthyretin, hemoglobin subunit alpha and hemoglobin sububit beta. The presence of these three biomarkers is associated with high Gleason scores and TNM stages but not with PSA level. Uromodulin and mannan binding lectin serine protease cancer from BPH. The study also revealed the divergence of the urinary proteome of the cancer patients from the urinary proteome of the control with BPH suggesting the fundamental differences in benign and malignant growth of the prostate epithelial cells. Another highlight of the study was the identification of oxidation of pro63 of transthyretin in patient 3. The proposed role of the post translational modification in pro63 of transthyretinin in the mechanism of prostate carcinogenesis remains to be defined and warrants further study.
CONCLUSION: Our study was able to establish the homology of urine proteome among the controls and its divergence from the patients afflicted with prostate cancer by simultaneously comparing their urine proteomes leading to the identification of a distinct panel of biomarkers, namely, transthyretin, hemoglobin subunit alpha and hemoglobin subunit beta. Uromodulin and mannan binding lectin serine protease 2 are the additional biomarkers that can distinguish prostate cancer from BPH. Due to limitations in the number of controls and patients, only preliminary findings and their significance were shown. These findings need to be confirmed in future investigations using larger sample size for both the controls and the patients.

Human ; Male ; Prostate-specific Antigen ; Proteome ; Proteomics ; Prealbumin ; Uromodulin ; Serine Proteases ; Mannose-binding Lectin ; Prostatic Neoplasms ; Carcinogenesis ; Peptides ; Hemoglobins ; Epithelial Cells

BACKGROUND: Evidence is conflicting regarding the effectiveness of creating a low-allergen environment or reducing allergen exposure to control asthma exacerbations. OBJECTIVE: This study determined the association of house dust mite (HDM)-specific IgE levels with asthma symptom control, selected medications, family history of allergic disease, and exposure to second-hand smoke and household pets. METHODS: Serum samples from 102 doctor-diagnosed allergic asthma patients and 100 non-atopic controls were subjected to enzyme-linked immunosorbent assay using the HDM species Dermatophagoides pteronyssinus (Dp), Dermatophagoides farinae (Df), and Blomia tropicalis (Bt) allergens. Point-biserial correlation coefficient, Pearson R correlation, and logistic regression analyses were used to determine association of HDM-specific IgE levels with the abovementioned variables. RESULTS: Of the 102 cases, 38.24%, 47.06%, and 33.33% were sensitized to Bt, Df, and Dp, respectively. Sensitized patients showed greater probability [Bt (OR = 1.21), Df (OR = 1.14), and Dp (OR = 1.35)] to manifest symptoms than those who were not. Obtained p-values [Bt (p = 0.73), Df (p = 0.83), and Dp (p = 0.59)], however, proved that HDM-specific IgE levels had no significant contribution in predicting or explaining occurrence of asthma symptoms. Bt- and Df-specific IgEs showed moderately weak but significant relationship with bambuterol HCl and expectorant, respectively. Patients currently on said medications registered higher HDM-specific IgE levels than those who were not. No significant correlation between IgE levels and family history of allergic disease or with exposure to second-hand smoke was seen. Dp-specific IgE levels of patients exposed to household pets were significantly lower compared to those without exposure. CONCLUSION: This study proves that sensitization to Bt, Df, and Dp allergens is not significantly associated with asthma symptoms and control. Although cases were shown to be sensitized to HDMs, their current medications were at least effective in controlling their asthma symptoms.
Allergens ; Asthma ; Dermatophagoides farinae ; Dermatophagoides pteronyssinus ; Dust ; Enzyme-Linked Immunosorbent Assay ; Family Characteristics ; Humans ; Immunoglobulin E ; Logistic Models ; Pyroglyphidae ; Smoke

BACKGROUND: Pollen grains have been reported to be present in the Philippine atmosphere but studies regarding their allergenicity are limited. OBJECTIVE: The present study aimed to profile the sensitization of allergic individuals to selected grass pollen species and to characterize the pollen proteins that may be responsible for this allergenic response. METHODS: The protein profile of the grass pollen extracts from Cynodon dactylon, Saccharum spontaneum, Sporobulus indicus, Chloris barbata, Oryza sativa, Imperata cylindrica, and Zea mays was analyzed by Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis. The specific-IgE profile of the allergic individuals and the allergenic potential of the pollen extracts were evaluated through Enzyme-linked Immunosorbent Assay and IgE immunoblotting. RESULTS: Sensitization of the allergic individuals to the pollen extracts was detected with I. cylindrica and O. sativa to be the most frequently recognized with more that 92% reactivity, whereas for C. dactylon and Z. mays, were found to have less than 25% reactivity. CONCLUSION: Multiple IgE-binding proteins from S. indicus, S. spontaneum and C. barbata that were detected may be responsible for the allergic reactions among Filipino subjects.
Atmosphere ; Cynodon ; Electrophoresis, Polyacrylamide Gel ; Enzyme-Linked Immunosorbent Assay ; Hypersensitivity ; Immunoblotting ; Immunoglobulin E ; Immunoglobulins ; Oryza ; Philippines ; Poaceae ; Pollen ; Saccharum ; Sodium ; Zea mays

Background: MicroRNAs (miRNA/miR) play significant roles in the regulation of cell differentiation, cell cycle progression, and apoptosis. They become dysregulated during carcinogenesis and are eventually released into the circulation, enabling their detection in body fluids. Thus, this study compared the miRNA expression in tissue and plasma samples of colorectal cancer (CRC) patients and clinically healthy controls and determined miRNA expression as a potential CRC biomarker. Methods: Using quantitative reverse transcription polymerase chain reaction (RT-qPCR), miR-21-5p, miR-29a-3p, miR-92a-3p, miR-135b-5p, miR-196b-5p, and miR-197-3p, expression was analyzed and compared between the malignant (n = 41) and the adjacent neoplasm free mucosal tissues (n = 41) of CRC patients. The findings were validated in plasma samples (n = 36) collected from the same CRC patients prior to surgery or any form of treatment and compared to plasma from their age and sex-matched controls (n = 36). Results: MiR-21-5p, miR-29a-3p, miR-92a-3p, and miR- 196b-5p were upregulated and miR-135b-5p was downregulated in CRC malignant tissues compared to their expression in adjacent neoplasm-free tissue. This was further observed in the plasma of the same CRC cases compared to controls. MiR-92a-3p showed itself the most sensitive (0.93; p < .001) and most specific (0.95; p < .001) in detecting CRC in tissue. In plasma, miR-196b-5p was the most sensitive (0.97; p < .001) and specific (0.94; p < .001) in detecting CRC. Plasma miR-92a-3p and miR-196b-5p were the most sensitive (0.95; p < .001) and specific (0.94; p < .001) in the early detection of CRC. Conclusions Results show that specific miRNAs dysregulated in malignanttissues are released and can be detected in the circulation, supporting their potential as non-invasive biomarkers of CRC.

BACKGROUND: Common antigens between intestinal parasites and environmental allergens may play a role in the modulation of allergic immune responses. There is a growing interest in investigating cross-reactivity between common helminths and dust mites affecting humans, particularly in the tropics. OBJECTIVE: This study examined the cross-reactivity between the human roundworm Ascaris lumbricoides (Al) and three house dust mite (HDM) species. METHODS: Specific serum IgE levels to HDM species Blomia tropicalis (Bt), Dermatophagoides pteronyssinus (Dp), and Dermatophagoides farinae (Df ); and Al extracts among allergic (n=100) and ascariasis (n=60) subjects were measured through enzyme-linked immunosorbent assay (ELISA). IgE-reactive components of HDM and Al extracts were detected through Western-Blot Analysis. Cross-reactivity between HDMs and Al was determined by ELISA inhibition using HDM and Al-specific sera from allergic (n=15) and ascariasis (n=15) subjects. The IgE-binding capacity of a recombinant paramyosin peptide (Blo t 11-fD) to allergic (n=50) and ascariasis (n=50) subjects' sera were likewise determined. RESULTS: Among allergic subjects, 70% exhibited Al-specific positive IgE-reactivity, while 20-28% of ascariasis subjects demonstrated HDM-specific positive IgE-reactivity. Multiple IgE-reactive components of HDM allergens (14-240 kDa) and Al antigens (15-250 kDa) were detected, indicating multi-allergen sensitization among the subjects tested. Al antigens can inhibit up to 92% of HDM-specific IgE-reactivity among allergic subjects, while up to 54% of Al-specific IgE-reactivity among ascariasis subjects was inhibited by HDM allergens. Positive rBlo t 11-fD-specific IgE reactivity was observed in 80% of the allergic subjects and 46% of the ascariasis subjects. CONCLUSIONS: This study showed the presence of multiple cross-reactive antigens in HDM and Al extracts. Identification of these molecules may provide basis for designing novel diagnostic and therapeutic strategies. The potential role of paramyosin as a specific cross-reactive allergen present in HDMs and Al has been shown.
Allergens ; Ascariasis ; Ascaris lumbricoides ; Ascaris ; Dermatophagoides farinae ; Dermatophagoides pteronyssinus ; Dust ; Enzyme-Linked Immunosorbent Assay ; Helminths ; Humans ; Immunoglobulin E ; Mites ; Parasites ; Pyroglyphidae ; Tropomyosin

BACKGROUND: The low prevalence of human papillomavirus (HPV) DNA and mRNA in biopsy samples of Filipinos with head and neck squamous cell carcinoma (HNSCC) has been reported previously. Here, the HPV serologic profiles of HNSCC cases were analyzed and associated with lifestyle and sexual practices. METHODS: Serum samples were collected between May 2012 and September 2013 from HNSCC patients (n = 22) in the northwest region of the Philippines, and age- and sex-matched clinically healthy controls. Antibodies to capsid and early oncoproteins of HPV16, 18, 31, 33, 45, 52, 58, 6, and 11 were analyzed using multiplex serology. RESULTS: Most of the cases were males with tumors of the oral cavity or larynx. Two of the cases tested positive for at least one of the early oncoproteins (E6, E7, E1, and/or E2) of HPV16, and 11 did not display reactivity to any HPV early or late oncoproteins. Of the controls, four tested positive for at least one of the HPV16 early oncoproteins, and 10 were non-reactive to all HPV types. Titers to HPV16 E6 or E7 of the seropositive cases and controls were considerably lower than those typically observed in economically developed countries. CONCLUSIONS: The low HPV titers seen here are consistent with the results of molecular analyses for this population. Hence, the seropositivity of some of the HNSCC cases is likely an indication of prior exposure to the virus and not the presence of HPV-driven tumors.
Antibodies ; Biopsy ; Capsid ; Carcinoma, Squamous Cell ; Developed Countries ; DNA ; Epithelial Cells ; Head ; Humans ; Larynx ; Life Style ; Male ; Mouth ; Neck ; Oncogene Proteins ; Philippines ; Prevalence ; RNA, Messenger