Michael Baclig | St. Luke's Medical Center (original) (raw)

Papers by Michael Baclig

In July, we asked young scientists to describe the one big idea in their field that they wish eve... more In July, we asked young scientists to describe the one big idea in their field that they wish every non-scientist understood

Non-alcoholic fatty liver disease (NAFLD) covers a spectrum of diseases from simple stea-tosis to... more Non-alcoholic fatty liver disease (NAFLD) covers a spectrum of diseases from simple stea-tosis to non-alcoholic steatohepatitis, with approximately 20% risk of progressing to fibrosis and cirrhosis. The aim of this study was to compare the relative expression levels of circulating miR-21, miR-34a, miR-122, miR-125b and miR-375 between healthy controls and NAFLD patients, and to assess the feasibility of microRNAs as potential biomarkers for NAFLD. A cross-sectional study was conducted to evaluate circulating serum miRNAs as potential diagnostic markers for NAFLD. Twenty-eight clinically diagnosed and histologi-cally-confirmed NAFLD patients, as well as 36 healthy controls were enrolled in this study. The relative expression of serum microRNAs were calculated using the comparative cycle threshold with spiked-in C. elegans miR-39 as exogenous internal control. Serum levels of miR-34a and miR-122 were significantly higher in NAFLD patients than in healthy controls (P = <0.0001). Positive correlations were observed between serum miR-34a with very low density lipoprotein cholesterol (VLDL-C) and triglyceride levels. However, the expression levels of miR-34a and miR-122 did not correlate with the histological features of NAFLD. Interestingly, receiver operating characteristic (ROC) curve analysis revealed that miR-34a and miR-122 are potential markers for discriminating NAFLD patients from healthy controls with an area under the curve (AUC) values of 0.781 and 0.858, respectively. Serum levels of miR-34a and miR-122 were found to be significantly higher among NAFLD patients, and were positively correlated with VLDL-C and triglyceride levels. Thus, circulating miR-34a and miR-122 can be used as potential biomarkers for discriminating NAFLD patients from healthy controls. Larger cohorts are required to validate the utility of miR-34a and miR-122 in monitoring liver injury.

Journal of Medical Virology, 2014

Point mutations and multiple variants across the a determinant can destroy the antigenicity and i... more Point mutations and multiple variants across the a determinant can destroy the antigenicity and immunogenicity of hepatitis B virus (HBV) leading to false negative assay and vaccine escape. In this study, the presence of surface gene variants of HBV was investigated among patients clinically diagnosed with chronic hepatitis B and positive for HBV DNA from 2002 to 2009. Sequence analysis of the surface gene of HBV showed that 23 (43%) of the 53 isolates had variations. Out of the 23 isolates, 15 (65%) exhibited single or multiple substitutions, which resulted to specific amino acid changes. The remaining 8 (35%) isolates had silent mutations. The amino acid substitution M133T which was associated with failure of HBsAg detection was found in one isolate (7%, 1/15), while the amino acid substitution D144A which was associated with vaccine escape was observed in one isolate (7%, 1/15). No G145R mutation was observed. Of the 15 isolates with identified single or multiple substitutions, 6 (40%) were found to have unique sequences which caused changes in the hydrophobicity profile in the protein. Unique sequence variants at amino acid positions M103I, L109P, S117R, F134I, and S136L found in this study have not yet been reported. These data should be taken into account when developing next generation HBV assays to detect both common and unique variants, and when new HBV vaccines will be designed.

Molecular Biology Reports, 2014

Hepatitis B virus (HBV) is one of the most prevalent viral infections worldwide. Nearly 400 milli... more Hepatitis B virus (HBV) is one of the most prevalent viral infections worldwide. Nearly 400 million individuals are chronic carriers of HBV. The aim of the present study was to determine the frequency of human interleukin 28B (IL28B) variants among treatment naive Filipino patients clinically diagnosed with chronic hepatitis B (CHB), and to compare the IL28B frequency distribution with various ethnic populations. Fifty-seven CHB patients and 43 normal controls were enrolled in this study. Real-time PCR was performed using the TaqMan genotyping assay for IL28B rs12979860. The allelic frequencies among normal controls were 0.94 and 0.06 for the IL28B rs12979860 C and T alleles, respectively. Eighty-eight percent were identified as homozygous for the IL28B C/C genotype and 12 % were identified as heterozygous for the IL28B C/T genotype. Among CHB patients, the allelic frequencies were 0.90 for the IL28B C allele and 0.10 for the IL28B T allele. No IL28B T/T genotype was observed between the two groups. No significant difference in the distribution of IL28B genotypes was observed between normal controls and CHB patients. Allelic frequencies of IL28B among Filipinos were similar with other Asian populations but significantly different from Caucasians. The frequency of rs12979860 C&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;gt;T variants among Filipino CHB patients has not yet been reported. These data provided new insight into the geographical frequency distribution of IL28B variants. Further studies are needed to determine the possible association between IL28B variants and response to pegylated-interferon-α plus ribavirin combination therapy among Filipino patients chronically infected with HBV.

International Journal of Clinical and Experimental Medicine

Genome-wide association studies have shown that a non-synonymous single nucleotide polymorphism c... more Genome-wide association studies have shown that a non-synonymous single nucleotide polymorphism characterized by a C-to-G change encoding an isoleucine-to-methionine substitution at amino acid position 148 in the human patatin-like phospholipase 3 (PNPLA3) gene was found to be associated with non-alcoholic fatty liver disease (NAFLD) and advanced liver damage. A hospital-based study was conducted to determine the distribution of PNPLA3 genotypes among patients clinically diagnosed and histologically confirmed with NAFLD and among normal controls. We also compared the allelic frequencies of PNPLA3 with different ethnic populations. More importantly, we evaluated the association between PNPLA3 genetic variation and risk of developing NAFLD among Filipinos. Real-time PCR was performed using the Taqman SNP genotyping assay for rs738409. Nucleotide sequencing was performed to confirm the PNPLA3 genotypes. Allelic frequencies among normal controls were 0.83 and 0.17 for the PNPLA3 C and P...

Chronic hepatitis B is a global health problem, and is one of the leading causes of cirrhosis and... more Chronic hepatitis B is a global health problem, and is one of the leading causes of cirrhosis and hepatocel-lular carcinoma. Hepatitis B virus (HBV) genotyping helps in decision making for clinical management of HBV infection , and is important for epidemiological studies. The objectives of this study were to investigate the distribution of HBV genotypes circulating in the Philippines; molecularly characterize untypable genotype restriction patterns; and analyze the presence of surface gene variants. HBV genotypes were determined by restriction fragment length polymorphism (RFLP) and DNA sequencing. Three genotypes, HBV A (76%; 73/96), HBV B (10%; 10/96) and HBV C (14%; 13/96) were detected by RFLP. Out of the 96 isolates, 9% were untypable by RFLP analysis. DNA sequencing followed by phylogenetic analysis revealed that these isolates belonged to HBV genotypes A (67%; 6/9), B (11%; 1/9) and C (22%; 2/9). Out of the 9 isolates, 55% showed single or multiple variations which resulted to amino acid changes. Overall, the identification of untypable genotype can be resolved by sequence and phylogenetic analysis of the S gene and this approach can also be used to detect single or multiple variants. Our findings underscore the importance of accurate genotyping and detection of surface gene variants by DNA sequencing for optimal clinical management.

The glutathione S-transferase (GST) supergene family is made up of four gene families responsible... more The glutathione S-transferase (GST) supergene family is made up of four gene families responsible for the
biotransformation of drugs and other xenobiotics. Genetic variations in this supergene family influence individual
detoxification levels and may contribute to the development of cancer. A hospital-based case-control study was conducted
to evaluate the association between GST polymorphism among Filipino patients positive for hepatitis B virus
(HBV DNA) and clinically diagnosed as either with chronic active hepatitis, liver cirrhosis, and hepatocellular carcinoma
as well as normal individuals negative for HBV infection. Multiplex PCR was used to detect the presence or
absence of the GSTT1 and GSTM1 polymorphisms in peripheral blood. DNA sequencing of the S gene region of the
virus was used to determine the predominant genotype found among HBV-infected patients. Our results showed that
the odds of having a chronic liver disease is only 0.95 (95% CI 0.58-1.57) among those with GSTT1 null genotype
compared to those with GSTT1+ genotype. On the other hand, the odds of chronic liver disease is 17.85 times (95%
CI 7.34-43.45) for those with GSTM1 null genotype compared to those with GSTM1+ genotype. Using the GSTT1+/
GSTM1+ genotype as the reference, both GSTT1+/GSTM1- (OR 16.61; 95% CI 6.69-41.22) and GSTT1-/GSTM1- (OR
11.91; 95% CI 4.48-31.66) genotypes seem to be risk factors for chronic liver disease. From our observations, we
conclude that polymorphism in GSTM1 null genotype (OR 17.85; 95% CI 7.34-43.45) seem to be associated with an
increased risk of chronic liver disease among Filipinos.

International journal of molecular epidemiology and genetics, 2012

A hospital-based cross-sectional study was conducted to determine the allelic and genotype freque... more A hospital-based cross-sectional study was conducted to determine the allelic and genotype frequencies in the genes encoding for catechol-O-methyltransferase and CYP2D6*10 among healthy volunteers and patients clinically diagnosed with cancer pain. PCR-RFLP was used to identify COMT and CYP2D6*10 genotypes. Allelic frequencies among healthy volunteer Filipinos were 0.83 and 0.17 for the COMT Val and COMT Met alleles, respectively. Calculated frequencies in Hardy-Weinberg equilibrium (HWE) were 73% for COMT Val/Val, 26% for COMT Val/Met, and 1% for COMT Met/Met genotype. For CYP2D6*10, allelic frequencies in HWE among volunteers were 0.46 for the C allele and 0.54 for the T allele. Twenty percent were identified as homozygous for the wild-type C/C genotype, 56% were identified as heterozygous for the C/T genotype, and 24% were identified as homozygous for the T/T variant genotype. No significant differences in COMT and CYP2D6*10 allele frequencies between cancer patients and healthy ...

International journal of molecular epidemiology and genetics, 2010

The 5'untranslated region (5'UTR) is often targeted to detect major genotypes in hepatiti... more The 5'untranslated region (5'UTR) is often targeted to detect major genotypes in hepatitis C virus (HCV) but its insufficient sequence variation limits its usefulness for differentiating HCV subtypes. Subtyping has important implications to epidemiologic studies, clinical management, and vaccine development. Analysis of the nucleotide sequence of variable regions such as the non-structural 5B (NS5B) is considered the reference method for identifying HCV subtypes. We evaluated the accuracy of subtyping of HCV genotype 1 (HCV-1) samples from the Philippines by 5'UTR sequencing as compared with the NS5B sequence. A total of 30 patients infected with HCV-1 previously confirmed by PCR-RFLP and clinically diagnosed with chronic hepatitis C were analyzed. Nucleotide sequencing of the 5'UTR showed that 15 (50%) were identified as 1a and 15 (50%) were identified as 1b. Sequence analysis of the NS5B revealed that 13 (43%) belonged to subtype 1a while 17 (57%) belonged to subty...

International Journal of Infectious Diseases, 2012

The non-structural 5B (NS5B) gene is the target region to identify hepatitis C virus (HCV) subtyp... more 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.

With the development of freeware bioinformatics software as well as the availability of web-based... more With the development of freeware bioinformatics software as well as the availability of web-based software, it is now possible to use various bioinformatics tools to identify viral subtypes such as hepatitis C virus (HCV). This study aimed to demonstrate the role of bioinformatics tools in identifying HCV subtypes and to compare the accuracy of HCV-1 subtyping by 5'UTR PCR-RFLP analysis and DNA sequencing. From a clinical viewpoint, accurate genotype and subtype identification of HCV are important because this may be used as guide for deciding which therapy is appropriate to use for a particular patient. From 2005 up to 2008, we had a total of 30 HCV genotype 1 (HCV-1) positive samples. HCV-1 subtypes were identified by an in-house PCR-RFLP analysis and through direct nucleic acid sequencing using nested primers specific to the 5'UTR and non-structural 5B (NS5B) region. Bioinformatics tools play an important role in identifying HCV-1 subtypes by predicting the size of the amplicon; determining the specific restriction enzyme to cut a given nucleic acid sequence; viewing and editing the electropherogram; aligning nucleotide sequences with prototypes; searching for identical sequences; and understanding the evolution and relationships of various subtypes. The HCV nucleotide sequences reported in this study have been deposited to GenBank. Overall, this information can be utilized to generate molecular diagnostic tests in the future.

The Southeast Asian journal of tropical medicine and public health, 2010

With the development of permeabilization techniques in flow cytometry and the availability of var... more With the development of permeabilization techniques in flow cytometry and the availability of various monoclonal antibodies (MAbs) that specifically bind with cell surface and intracellular antigens, it is now possible to use flow cytometric assay to identify dengue virus (DEN) infected cells in peripheral blood. Blood samples were analyzed using phycoerythrin (PE) labeled anti-CD3, anti-CD14, anti-CD16, and anti-CD19 antibodies and Alexa Fluor 488 labeled anti-flavivirus monoclonal antibody (MAb) 6B6C-1. The predominant DEN-infected cells were CD19+ in this study. There was dim partial to moderately bright partial expression of CD19 positive cells in the blood samples tested. Virus isolation and serotype-specific RT-PCR revealed the cells were infected with dengue serotype 3 (DEN3). Our results suggest B cells may play an important role in DEN1 and DEN3 replication, and dissemination in vivo.

The Southeast Asian journal of tropical medicine and public health, 2008

We report a case of a 45-year old Filipino post-kidney transplant patient maintained on steroids,... more We report a case of a 45-year old Filipino post-kidney transplant patient maintained on steroids, who presented with floaters in her left eye. Vitreous aspirate was analyzed using polymerase chain reaction (PCR) for human cytomegalovirus (HCMV) and herpes simplex virus (HSV). A distinct band (435 bp) was found that confirmed the presence of HCMV. Since a rapid and accurate diagnosis is crucial for prompt administration of antiviral therapy, PCR-based analysis of vitreous aspirate provides a valuable tool in the diagnosis of patients with retinitis caused by herpes viruses.

Tropical Medicine and Health, 2014

We report the case of a 76-year old Filipino male who presented with pain, redness, and blurring ... more We report the case of a 76-year old Filipino male who presented with pain, redness, and blurring of vision of the right eye. Corneal scraping was done and sent to the St. Luke's Research and Biotechnology Group for detection and identification of the infectious agent. Morphological detection was performed by allowing the organism from the scraping to grow in 1.5% non-nutrient agar plate with heat-killed E. coli. Trophozoites with acanthopodia and double-walled cysts characteristic of Acanthamoeba were observed within the first and second week of observations, respectively. Molecular identification of the amoebae at the genus level based on the presence of Acanthamoeba-specific amplimer S1, ASA.S1 confirmed the morphological identification. Genotyping through sequence revealed that the organism belonged to T4, which is the genotype commonly present in the eye of keratitis patients.

Genome-wide association studies (GWAS) have emerged as a novel and powerful genotyping technique ... more Genome-wide association studies (GWAS) have emerged as a novel and powerful genotyping technique to identify risk variants for complex traits. The objective of this article is to provide an overview of GWAS and summarize the recent discoveries identified by GWAS for various kidney diseases.