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Analysis of differentially expressed proteins in cancerous and normal colonic tissues

Gam LH, Leow CH, Man CN, Gooi BH, Singh M

World J Gastroenterol, 2006 Aug 21;12(31):4973-80.
PMID: 16937492

AIM: To identify and analyze the differentially expressed proteins in normal and cancerous tissues of four patients suffering from colon cancer.
METHODS: Colon tissues (normal and cancerous) were homogenized and the proteins were extracted using three protein extraction buffers. The extraction buffers were used in an orderly sequence of increasing extraction strength for proteins with hydrophobic properties. The protein extracts were separated using the SDS-PAGE method and the images were captured and analyzed using Quantity One software. The target protein bands were subjected to in-gel digestion with trypsin and finally analyzed using an ESI-ion trap mass spectrometer.
RESULTS: A total of 50 differentially expressed proteins in colonic cancerous and normal tissues were identified.
CONCLUSION: Many of the identified proteins have been reported to be involved in the progression of similar or other types of cancers. However, some of the identified proteins have not been reported before. In addition, a number of hypothetical proteins were also identified.
Analysis of differentially expressed proteins in colorectal cancer using hydroxyapatite column and SDS-PAGE

Lim SR, Gooi BH, Singh M, Gam LH

Appl Biochem Biotechnol, 2011 Nov;165(5-6):1211-24.
PMID: 21863284 DOI: 10.1007/s12010-011-9339-3

Limitation on two dimensional (2D) gel electrophoresis technique causes some proteins to be under presented, especially the extreme acidic, basic, or membrane proteins. To overcome the limitation of 2D electrophoresis, an analysis method was developed for identification of differentially expressed proteins in normal and cancerous colonic tissues using self-pack hydroxyapatite (HA) column. Normal and cancerous colon tissues were homogenized and proteins were extracted using sodium phosphate buffer at pH 6.8. Protein concentration was determined and the proteins were loaded unto the HA column. HA column reduced the complexity of proteins mixture by fractionating the proteins according to their ionic strength. Further protein separation was accomplished by a simple and cost effective sodium dodecyl sulfate-polyacrylamide gel electrophoresis method. The protein bands were subjected to in-gel digestion and protein analysis was performed using electrospray ionization (ESI) ion trap mass spectrometer. There were 17 upregulated proteins and seven downregulated proteins detected with significant differential expression. Some of these proteins were low abundant proteins or proteins with extreme pH that were usually under presented in 2D gel analysis. We have identified brain mitochondrial carrier protein 1, T-cell surface glycoprotein CD1a, SOSS complex subunit B2, and Protein Jade 1 which were previously not detected in 2D gel analysis method.
Analysis of differentially expressed proteins in late-stationary growth phase of Mycobacterium tuberculosis H37Rv

Ang KC, Ibrahim P, Gam LH

Biotechnol Appl Biochem, 2014 Mar-Apr;61(2):153-64.
PMID: 23826872 DOI: 10.1002/bab.1137

Mycobacterium tuberculosis is a causative agent of tuberculosis (TB). The ability of M. tuberculosis to be quiescent in the cell has caused the emergence of latent infection. A comprehensive proteomic analysis of M. tuberculosis H37Rv over three growth phases, namely mid-log (14-day culture), early stationary (28-day culture), and late stationary (50-day culture), was performed in order to study the change in proteome from the mid-log phase to late-stationary phase. Combination methods of two-dimensional electrophoresis (2-DE) and tandem mass spectrometry were used to generate proteome maps of M. tuberculosis at different growth phases. Ten proteins were detected differentially expressed in the late-stationary phase compared with the other two phases. These proteins were SucD, TrpD, and Rv2161c, which belong to metabolic pathway proteins; FadE5, AccD5, DesA1, and Rv1139c are proteins involved in cell wall or lipid biosynthesis, whereas TB21.7 and Rv3224 are conserved hypothetical proteins with unknown function. A surface antigen protein, DesA1, was not detectable in the late-stationary phase, although present in both log and early-stationary phases. The changes in the expression levels of these proteins were in line with the growth environment changes of the bacteria from mid-log phase to late-stationary phase. The information gathered may be valuable in the intervention against latent TB infection.
Fulltext Breast cancer and protein biomarkers

Gam LH

World J Exp Med, 2012 Oct 20;2(5):86-91.
PMID: 24520539 DOI: 10.5493/wjem.v2.i5.86

Breast cancer is a healthcare concern of women worldwide. Despite procedures being available for diagnosis, prognosis and treatment of breast cancer, researchers are working intensively on the disease in order to improve the life quality of breast cancer patients. At present, there is no single treatment known to bring a definite cure for breast cancer. One of the possible solutions for combating breast cancer is through identification of reliable protein biomarkers that can be effectively used for early detection, prognosis and treatments of the cancer. Therefore, the task of identification of biomarkers for breast cancer has become the focus of many researchers worldwide.
Characterization of urinary protein profile in regular kratom (Mitragyna speciosa korth.) users in Malaysia

Jasim RK, Hassan Z, Singh D, Boyer E, Gam LH

J Addict Dis, 2021 Nov 08.
PMID: 34747343 DOI: 10.1080/10550887.2021.1981122

Mitragyna speciosa (Korth.) also known as kratom or ketum has been traditionally used for its diverse medicinal value in Southeast Asia. Despite of its therapeutic value, kratom's safety profile remains deficiently elucidated. Our study aims to characterize the urinary protein profile of regular kratom users to determine its toxic effects on renal functioning. A total of 171 respondents (comprising of n = 88 regular kratom users, and n = 83 healthy controls) were recruited for this study. Urine specimens were collected and analyzed using SDS-PAGE, followed by LC/MS/MS analysis. Our results show albumin is the primary, and most abundant form of protein excreted in kratom user's urine specimens (n = 60/64), indicating that kratom users are predisposed to proteinuria. Kratom users had an elevated urinary protein (with an intensity of 66.7 kDa band), and protein: creatinine ratio (PCR) concentrations relative to healthy controls. However, kratom user's urinary creatinine concentration was found to be in the normal range as the healthy control group. While, kratom users who tested positive for illicit drug use had an elevated urinary albumin concentration. Our preliminary findings indicate that regular consumption of freshly brewed kratom solution over a protracted period (for an average of eleven years) seems to induce proteinuria, suggestive of an early stage of kidney injury. Hence, further studies are urgently needed to confirm our findings, and establish kratom's renal impairing effects.
Fulltext Chemometrics of differentially expressed proteins from colorectal cancer patients

Yeoh LC, Dharmaraj S, Gooi BH, Singh M, Gam LH

World J Gastroenterol, 2011 Apr 28;17(16):2096-103.
PMID: 21547128 DOI: 10.3748/wjg.v17.i16.2096

To evaluate the usefulness of differentially expressed proteins from colorectal cancer (CRC) tissues for differentiating cancer and normal tissues.
Cloning, expression and purification of squalene synthase from Candida tropicalis in Pichia pastoris

Lee PY, Yong VC, Rosli R, Gam LH, Chong PP

Protein Expr Purif, 2014 Feb;94:15-21.
PMID: 24184232 DOI: 10.1016/j.pep.2013.10.012

Squalene synthase (SS) is the key precursor and first committed enzyme of the sterol biosynthesis pathway. In a previous work, SS has been identified as one of the immunogenic proteins that could be a potential diagnostic candidate for the pathogenic fungus Candida tropicalis. In this study, SS from C. tropicalis was cloned and expressed as recombinant protein in Pichia pastoris to investigate its reactivity with serum antibodies. ERG9 gene that encodes for SS was amplified by PCR and cloned in-frame into pPICZB expression vector. The recombinant construct was then transformed into P. pastoris GS115 host strain. Expression of the recombinant protein was confirmed by SDS-PAGE and Western blot analysis using anti-His tag probe. Optimal protein production was achieved by cultivating the culture with 1.0% methanol for 72h. The recombinant protein was purified to approximately 97% pure in a single step immobilized metal affinity chromatography with a yield of 70.3%. Besides, the purified protein exhibited specific reactivity with immune sera on Western blot. This is the first report on heterologous expression of antigenic SS from C. tropicalis in P. pastoris which can be exploited for large-scale production and further research. The results also suggested that the protein might be of great value as antigen candidate for serodiagnosis of Candida infection.
Fulltext Comparison of protein expression profiles of different stages of lymph nodes metastasis in breast cancer

Lee HH, Lim CA, Cheong YT, Singh M, Gam LH

Int J Biol Sci, 2012;8(3):353-62.
PMID: 22393307 DOI: 10.7150/ijbs.3157

Breast cancer is the most common cancer among women worldwide. Breast cancer metastasis primarily happens through lymphatic system, where the extent of lymph node metastasis is the major factor influencing staging, prognosis and therapeutic decision of the disease. We aimed to study the protein expression changes in different N (regional lymph nodes) stages of breast cancer. Protein expression profiles of breast cancerous and adjacent normal tissues were mapped by proteomics approach that comprises of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and tandem mass spectrometry (LC-MS/MS) analysis. Calreticulin and tropomyosin alpha 3 chains were the common up-regulated proteins in N0, N1 and N2 stages of breast cancer. Potential biomarker for each N stage was HSP 70 for N0, 80 k protein H precursor and PDI for N1 stage while 78 kDa glucose-regulated protein was found useful for N2 stage. In addition, significant up-regulation of PDI A3 was detected only in the metastasized breast cancer. The up-regulation expression of these proteins in cancerous tissues can potentially use as indicators for diagnosis, treatment and prognosis of different N stages of breast cancer.
Detection of antibodies against Salmonella typhi outer membrane protein (OMP) preparation in typhoid fever patients

Verdugo-Rodriguez A, Gam LH, Devi S, Koh CL, Puthucheary SD, Calva E, et al.

Asian Pac J Allergy Immunol, 1993 Jun;11(1):45-52.
PMID: 8216558

An indirect ELISA was used to detect antibodies against outer membrane protein preparations (OMPs) from Salmonella typhi. Sera from patients with a definitive diagnosis of typhoid fever (TF) gave a mean absorbance reading, at 414 nm, of 1.52 +/- 0.23 as compared to 0.30 +/- 0.11 for sera from healthy individuals. This gave a positive to negative ratio of absorbance readings of approximately 5.1. Suspected TF patients (no isolation of S. typhi), with positive and negative Widal titers had mean absorbance readings of 1.282 +/00.46 and 0.25 +/- 0.19, respectively. Sera from patients with leptospirosis, rickettsial typhus, dengue fever, and other infections gave mean absorbances of 0.20 +/- 0.08, 0.24 +/- 0.08, 0.27 +/- 0.08, and 0.31 +/- 0.16, respectively. The sensitivity, specificity, positive and negative predictive values were 100%, 94%, 80% and 100%, respectively. The antibody response detected in the definitive TF cases was predominantly IgG in nature and no cross-reactivity was seen with OMP preparations extracted from E. coli. Variable reactivity was noted with OMP preparations obtained from other Salmonella spp. Three major OMPs are presented in the antigen preparation and strong binding of positive sera was detected to all three bands.
Development and validation of ELISA for screening of Kratom (Mitragyna speciosa) habitual users using urinary AZ122 biomarker

Jasim RK, Singh D, Gam LH

Biotechnol Appl Biochem, 2023 Apr;70(2):707-715.
PMID: 35931067 DOI: 10.1002/bab.2392

Kratom (Mitragyna speciosa Korth) has been used traditionally in Southeast Asia for its therapeutic properties. The major alkaloid of kratom, mitragynine, binds to opioid receptors to give opioid-like effects that causes addiction. In our previous study, we have identified AZ122 as a unique biomarker in habitual or regular kratom users through analysis of their urinary protein profiles. We aimed to develop and validate a screening method by means of enzyme-linked immunosorbent assay (ELISA) for detection of kratom habitual users. An ELISA approach was applied for the development of a screening method using urinary AZ122 as biomarker. Method validation was carried out using three quality control materials at different concentration of AZ122. The data was analyzed statistically using SPSS (Version 25). The ELISA was presented with Pearson correlation coefficient of 0.9993. The repeatability and reproducibility were presented at CV <7%, while the accuracy ranged from 78 to 96% at various AZ112 concentrations. Upon testing on 176 male respondents (n = 88 regular kratom users and n = 88 healthy controls), the specificity and sensitivity of the assay were both 100%. The ELISA has been validated and can be potentially used as a reliable screening test for detection of kratom habitual users.
Differentiation of bovine from porcine gelatin capsules using gel electrophoresis method

Yap BK, Gam LH

Food Chem, 2019 Feb 15;274:16-19.
PMID: 30372921 DOI: 10.1016/j.foodchem.2018.08.111

Gelatin is commonly used in food supplements and in the form of soft or hard capsules. The source of gelatins is usually from porcine and bovine, and less commonly from vegetable and fish. Nevertheless, these different origins of gelatin have much similarity in term of structures, physicochemical properties and amino acid sequences. Due to these reasons, differentiation of the source of gelatins has been very difficult. In our present study, differentiation of sources of gelatin was made possible in a simplified yet economical method. Sample was prepared using ammonium sulfate precipitation and subjected to gel electrophoresis for protein separation. We have found a fraction of proteins which is able to differentiate porcine and bovine gelatins accurately, with distinctive protein bands in SDS-PAGE at 140 kDa and 110 kDa for bovine and porcine samples, respectively. This method was verified by 13 double-blinded gelatin samples, all the 13 samples were accurately identified.
Hydrophobic protein in colorectal cancer in relation to tumor stages and grades

Yeoh LC, Loh CK, Gooi BH, Singh M, Gam LH

World J Gastroenterol, 2010 Jun 14;16(22):2754-63.
PMID: 20533595

AIM: To identify differentially expressed hydrophobic proteins in colorectal cancer.
METHODS: Eighteen pairs of colorectal cancerous tissues in addition to tissues from normal mucosa were analysed. Hydrophobic proteins were extracted from the tissues, separated using 2-D gel electrophoresis and analysed using Liquid Chromatography Tandem Mass Spectrometry (LC/MS/MS). Statistical analysis of the proteins was carried out in order to determine the significance of each protein to colorectal cancer (CRC) and also their relation to CRC stages, grades and patients' gender.
RESULTS: Thirteen differentially expressed proteins which were expressed abundantly in either cancerous or normal tissues were identified. A number of these proteins were found to relate strongly with a particular stage or grade of CRC. In addition, the association of these proteins with patient gender also appeared to be significant.
CONCLUSION: Stomatin-like protein 2 was found to be a promising biomarker for CRC, especially in female patients. The differentially expressed proteins identified were associated with CRC and may act as drug target candidates.
Identification of immunogenic proteins of Candida parapsilosis by serological proteome analysis

Lee PY, Gam LH, Yong VC, Rosli R, Ng KP, Chong PP

J Appl Microbiol, 2014 Apr;116(4):999-1009.
PMID: 24299471 DOI: 10.1111/jam.12408

Systemic candidiasis is the leading fungal bloodstream infection, and its incidence has been on the rise. Recently, Candida parapsilosis has emerged as an increasingly prevalent fungal pathogen, but little is known about its antigenic profile. Hence, the current work was performed to discover immunogenic proteins of C. parapsilosis using serological proteome analysis.
Identification of low abundance proteins in colorectal cancer tissues

Lim SR, Gooi BH, Gam LH

Cancer Biomark, 2012;12(4):185-98.
PMID: 23568009 DOI: 10.3233/CBM-130307

Detection of low abundance proteins always possesses challenges even with the currently available proteomics technologies.
Identification of urinary protein biomarkers for tobacco smoking

Haniff AN, Gam LH

Biotechnol Appl Biochem, 2016 Mar;63(2):266-72.
PMID: 25640279 DOI: 10.1002/bab.1357

Smoking, passive smoking, and nonsmoking are conditions that give different degrees of stress to the body. In this study, a proteomic technique was used to analyze differentially urinary protein expression between these three groups of subjects. Urinary proteins were precipitated using ammonium sulfate followed by separation according to molecular weights using SDS-PAGE. The gel was stained by Coommassie blue, and the image of the gel was captured for the comparison study. The protein bands that were consistently detected but expressed at different intensity between the smokers and nonsmokers were targeted for further analysis. Three targeted protein bands were excised from the gel, consisting of a unique protein band of smokers and a pair of differentially expressed protein bands from smokers and nonsmokers. The proteins were digested in gel by trypsin. The tryptic peptides were analyzed with ultra performance liquid chromatography-tandem mass spectrometry. Protein identity was determined by the product ion spectrum in the MS/MS scan. Four unique proteins from the smokers, namely, pancreatic alpha amylase, proepidermal growth factor, protein 4.1, and prostatic acid phosphatase, were found to be potential urinary biomarkers to indicate smoking status of a person.
Immunoaffinity extraction and tandem mass spectrometric analysis of human chorionic gonadotropin in doping analysis

Gam LH, Tham SY, Latiff A

J Chromatogr B Analyt Technol Biomed Life Sci, 2003 Jul 25;792(2):187-96.
PMID: 12860026

A confirmatory and quantitative HPLC-tandem mass spectrometry (MS-MS) method for human chorionic gonadotropin hormone (hCG) at concentrations as low as 5 IU/l following immunoaffinity extraction of the glycoprotein from urine was developed. The extraction method involved retention of urinary hCG in the immunoaffinity column via specific antigen-antibody interaction. A variety of eluents were then used to quantitatively elute hCG from the immunoaffinity column. Qualitative and quantitative analysis of hCG were undertaken using MS-MS by identifying the amino acid sequence of the marker peptide betaT5 obtained from hCG by tryptic digestion and the peak areas of three product ions b(6)(+), b(9)(+) and y(11)(+), respectively.
Immunoproteomic analysis of antibody response to cell wall-associated proteins of Candida tropicalis

Lee PY, Gam LH, Yong VC, Rosli R, Ng KP, Chong PP

J Appl Microbiol, 2014 Sep;117(3):854-65.
PMID: 24909754 DOI: 10.1111/jam.12562

This study was conducted to identify antigenic proteins of Candida tropicalis that are targeted by the host immune system.
Method development for analysis of proteins extracted from the leaves of Orthosiphon aristatus

Koay SY, Gam LH

J Chromatogr B Analyt Technol Biomed Life Sci, 2011 Jul 15;879(22):2179-83.
PMID: 21689998 DOI: 10.1016/j.jchromb.2011.05.041

Orthosiphon aristatus is a traditionally used medicinal plant. In order to study the proteome of the plant, we have developed a simple plant protein extraction method by direct extraction of protein using a modified 2D-gel compatible tris-sucrose buffer followed by a double TCA-acetone precipitation. This method omitted the use of toxic phenol which is widely used in the studies of plants proteins. Moreover, it shortens the lengthy extraction procedure of phenol extraction and back-extraction method and therefore reduced the extraction time (by 2h) while increased in protein yields (by 50%). Comparison of the 2D-gel images of the two extracts revealed that >60 extra protein spots were detected in the extract of our current method. The method was applied on the leaves of O. aristatus collected from six geographical areas in Malaysia. The correlation coefficient of each replicate gels from the six areas ranged from 0.70 to 0.90 indicating good reproducibility of the method.
Fulltext Modulation of interleukin-18 release produced positive outcomes on parasitaemia development and cytokines production during malaria in mice

Basir R, Hasballah K, Jabbarzare M, Gam LH, Abdul Majid AM, Yam MF, et al.

Trop Biomed, 2012 Sep;29(3):405-21.
PMID: 23018504 MyJurnal

The involvement of interleukin-18 (IL-18) and the effects of modulating its release on the course of malaria infection were investigated using Plasmodium berghei ANKA infection in ICR mice as a model. Results demonstrated that plasma IL-18 concentrations in malarial mice were significantly elevated and positively correlated with the percentage parasitaemia development. Significant expressions of IL-18 were also observed in the brain, spleen and liver tissues. Slower development of parasitaemia was observed significantly upon inhibition and neutralization of IL-18, whereas faster development of parasitaemia was recorded when the circulating levels of IL-18 were further augmented during the infection. Inhibition and neutralization of IL-18 production also resulted in a significant decrease of plasma concentrations of pro-inflammatory cytokines (TNFα, IFNγ, IL-1α and IL-6), whereas the anti-inflammatory cytokine, IL-10, was significantly increased. Augmenting the release of IL- 18 during the infection on the other hand resulted in the opposite. Early mortality in malarial mice was also observed when the circulating levels of IL-18 were further augmented. Results proved the important role of IL-18 in immune response against malaria and suggest that IL-8 is pro-inflammatory in nature and may involve in mediating the severity of the infection through a pathway of elevating the pro-inflammatory cytokine and limiting the release of anti-inflammatory cytokine.
Potential hydrophobic protein markers of breast cancer in Malaysian Chinese, Malay and Indian patients

Liang S, Singh M, Gam LH

Cancer Biomark, 2010;8(6):319-30.
PMID: 22072120 DOI: 10.3233/CBM-2011-0221

Breast cancer is a leading cause of worldwide mortality in females. In Malaysia, breast cancer is the most commonly diagnosed cancer in women. Of these, the Chinese had the most number of breast cancer cases, followed by the Indian and the Malay. The most common type of breast cancer is infiltrating ductal carcinoma (IDC). A proteomic approach was used to identify protein profile changes in cancerous tissues compared with the normal tissues, the tissues were collected from patients of three different ethnicities, i.e. Chinese, Malay and Indian. Ten differentially expressed hydrophobic proteins were identified. We had evaluated the potential of these proteins as biomarker for infiltrating ducal carcinoma (IDC) and the ethnic-specific expression of these proteins was also determined. The data showed that peroxiredoxin-2, heat shock protein 60, protein disulfide isomerase and calreticulin may serve as ethnic-related potential markers for either one or combination of Chinese, Malay and Indian cohorts as their expression levels were significantly high in the cancerous tissues compared to the normal tissues in the ethnic group tested.
Publication year=2010-2011

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