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Fulltext The assessment of risk factors for the Central/East African Genotype of chikungunya virus infections in the state of Kelantan: a case control study in Malaysia

Yusoff AF, Mustafa AN, Husaain HM, Hamzah WM, Yusof AM, Harun R, et al.

BMC Infect Dis, 2013 May 08;13:211.
PMID: 23656634 DOI: 10.1186/1471-2334-13-211

BACKGROUND: The aims of the study were to assess the risk factors in relation to cross border activities, exposure to mosquito bite and preventive measures taken.An outbreak of chikungunya virus (CHIKV) infection in Malaysia has been reported in Klang, Selangor (1998) and Bagan Panchor, Perak (2006). In 2009, CHIKV infection re-emerged in some states in Malaysia. It raises the possibilities that re-emergence is part of the epidemics in neighbouring countries or the disease is endemic in Malaysia. For this reason, A community-based case control study was carried out in the state of Kelantan.
METHODS: Prospective case finding was performed from June to December 2009. Those who presented with signs and symptoms of CHIKV infection were investigated. We designed a case control study to assess the risk factors. Assessment consisted of answering questions, undergoing a medical examination, and being tested for the presence of IgM antibodies to CHIKV. Descriptive epidemiological studies were conducted by reviewing both the national surveillance and laboratory data. Multivariable logistic regression analysis was performed to determine risk factors contributing to the illness. Cases were determined by positive to RT-PCR or serological for antibodies by IgM. CHIKV specificity was confirmed by DNA sequencing.
RESULTS: There were 129 suspected cases and 176 controls. Among suspected cases, 54.4% were diagnosed to have CHIKV infection. Among the controls, 30.1% were found to be positive to serology for antibodies [IgM, 14.2% and IgG, 15.9%]. For analytic study and based on laboratory case definition, 95 were considered as cases and 123 as controls. Those who were positive to IgG were excluded. CHIKV infection affected all ages and mostly between 50-59 years old. Staying together in the same house with infected patients and working as rubber tappers were at a higher risk of infection. The usage of Mosquito coil insecticide had shown to be a significant protective factor. Most cases were treated as outpatient, only 7.5% needed hospitalization. The CHIKV infection was attributable to central/east African genotype CHIKV.
CONCLUSIONS: In this study, cross border activity was not a significant risk factor although Thailand and Malaysia shared the same CHIKV genotype during the episode of infections.
Fulltext History of Neurosurgery in Malaysia: The Past, Present and Future

Abdullah FC, Zakaria Z, Thambinayagam HC, Kandasamy R, Alias A, Abu Bakar A, et al.

Malays J Med Sci, 2021 Dec;28(6):129-185.
PMID: 35002497 DOI: 10.21315/mjms2021.28.6.13

The history of neurosurgery in Malaysia traces back to 1962 and is filled with stories of vibrant and humble neurosurgeons who have dedicated their life to patients and professions. The early development of neurological and neurosurgical services begins from the establishment of the neurosurgery unit at Hospital Kuala Lumpur (HKL), followed by the foundation of the Tunku Abdul Rahman Neuroscience Institute (IKTAR). Due to the exponentially increased demand for the care of neurosurgical patients, many universities and government hospitals have opened their neurosurgical units. In 2001, the formal residency training programme (USM Masters in Neurosurgery) started and since then has produced qualified neurosurgeons that empowered and shaped the present generation. The formation of the Neurosurgical Association of Malaysia (NAM) is another turning point towards bidirectional collaboration with the World Federation of Neurosurgical Societies (WFNS). Many opportunities were created for educational activities and the expansion of subspecialties in neurosurgery. This article describes the impact of the past neurosurgeons and the endeavors that they had gone through; the present neurosurgeons who pioneered the current neurosurgical services in Malaysia, and the future neurosurgeons that will continue the legacy and bring neurosurgery further ahead in this country.
Fulltext Screening of native microalgae species for carbon fixation at the vicinity of Malaysian coal-fired power plant

Yahya L, Harun R, Abdullah LC

Sci Rep, 2020 12 18;10(1):22355.
PMID: 33339883 DOI: 10.1038/s41598-020-79316-9

Global warming has become a serious issue nowadays as the trend of CO2 emission is increasing by years. In Malaysia, the electricity and energy sector contributed a significant amount to the nation's CO2 emission due to fossil fuel use. Many research works have been carried out to mitigate this issue, including carbon capture and utilization (CCUS) technology and biological carbon fixation by microalgae. This study makes a preliminary effort to screen native microalgae species in the Malaysian coal-fired power plant's surrounding towards carbon fixation ability. Three dominant species, including Nannochloropsis sp., Tetraselmis sp., and Isochrysis sp. were identified and tested in the laboratory under ambient and pure CO2 condition to assess their growth and CO2 fixation ability. The results indicate Isochrysis sp. as the superior carbon fixer against other species. In continuation, the optimization study using Response Surface Methodology (RSM) was carried out to optimize the operating conditions of Isochrysis sp. using a customized lab-scale photobioreactor under simulated flue gas exposure. This species was further acclimatized and tested under actual flue gas generated by the power plant. Isochrysis sp. had shown its capability as a carbon fixer with CO2 fixation rate of 0.35 gCO2/L day under actual coal-fired flue gas exposure after cycles of acclimatization phase. This work is the first to demonstrate indigenous microalgae species' ability as a carbon fixer under Malaysian coal-fired flue gas exposure. Thus, the findings shall be useful in exploring the microalgae potential as a biological agent for carbon emission mitigation from power plants more sustainably.
Algal biomass conversion to bioethanol - a step-by-step assessment

Harun R, Yip JW, Thiruvenkadam S, Ghani WA, Cherrington T, Danquah MK

Biotechnol J, 2014 Jan;9(1):73-86.
PMID: 24227697 DOI: 10.1002/biot.201200353

The continuous growth in global population and the ongoing development of countries such as China and India have contributed to a rapid increase in worldwide energy demand. Fossil fuels such as oil and gas are finite resources, and their current rate of consumption cannot be sustained. This, coupled with fossil fuels' role as pollutants and their contribution to global warming, has led to increased interest in alternative sources of energy production. Bioethanol, presently produced from energy crops, is one such promising alternative future energy source and much research is underway in optimizing its production. The economic and temporal constraints that crop feedstocks pose are the main downfalls in terms of the commercial viability of bioethanol production. As an alternative to crop feedstocks, significant research efforts have been put into utilizing algal biomass as a feedstock for bioethanol production. Whilst the overall process can vary, the conversion of biomass to bioethanol usually contains the following steps: (i) pretreatment of feedstock; (ii) hydrolysis; and (iii) fermentation of bioethanol. This paper reviews different technologies utilized in the pretreatment and fermentation steps, and critically assesses their applicability to bioethanol production from algal biomass. Two different established fermentation routes, single-stage fermentation and two-stage gasification/fermentation processes, are discussed. The viability of algal biomass as an alternative feedstock has been assessed adequately, and further research optimisation must be guided toward the development of cost-effective scalable methods to produce high bioethanol yield under optimum economy.
Fulltext COSMO-RS Based Prediction for Alpha-Linolenic Acid (ALA) Extraction from Microalgae Biomass Using Room Temperature Ionic Liquids (RTILs)

Rezaei Motlagh S, Harun R, Awang Biak DR, Hussain SA, Omar R, Elgharbawy AA

Mar Drugs, 2020 Feb 12;18(2).
PMID: 32059424 DOI: 10.3390/md18020108

One of the essential fatty acids with therapeutic impacts on human health is known to be omega-3 polyunsaturated fatty acids (PUFA). More lately, ionic liquids (ILs) have received significant attention among scientists in overcoming the disadvantages of traditional solvents in biomass lipid extraction. However, the large pool of cations and anions possibly accessible will lead to a growing number of innovatively synthesized ILs. Nevertheless, the exhaustive measurement of all these systems is economically impractical. The conductive screening model for real solvents (COSMO-RS) is considered a precious approach with the availability of a few models to predict the characteristics of ILs. This work introduces the estimate of capacity values at infinite dilution for a range of ILs using COSMO-RS software as part of solid-liquid extraction. This favorable outcome presented that the capacity values of the IL molecules are extremely dependent on both anions and cations. Among the 352 combinations of cation/anion tested, short alkyl chain cations coupled with inorganic anions were found to be most efficient and therefore superior in the extraction method. Sulphate-, chloride-, and bromide-based ILs were found to have higher extraction capacities in contrast with the remainders, while propanoate revealed an extraordinary capacity when combined with ethyl-based cations. Eventually, the predicted results from COSMO-RS were validated through the experimentally calculated extraction yield of alpha-linolenic acid (ALA) compound from Nannochloropsis sp. microalgae. Three selected ILs namely [EMIM][Cl], [TMAm][Cl], and [EMPyrro][Br] were selected from COSMO-RS for empirical extraction purpose and the validation results pinpointed the good prediction capability of COSMO-RS.
Fulltext Subcritical Water Extraction of Chlorella pyrenoidosa: Optimization through Response Surface Methodology

Thiruvenkadam S, Izhar S, Hiroyuki Y, Harun R

Biomed Res Int, 2018;2018:1931634.
PMID: 30533428 DOI: 10.1155/2018/1931634

Subcritical water extraction (SCW) was used to extract oil from Chlorella pyrenoidosa. The operational factors such as reaction temperature, reaction time, and biomass loading influence the oil yield during the extraction process. In this study, response surface methodology was employed to identify the desired extraction conditions for maximum oil yield. Experiments were carried out in batch reactors as per central composite design with three independent factors including reaction temperature (170, 220, 270, 320, and 370°C), reaction time (1, 5, 10, 15, and 20 min), and biomass loading (1, 3, 5, 10, and 15%). A maximum oil yield of 12.89 wt.% was obtained at 320°C and 15 min, with 3% biomass loading. Sequential model tests showed the good fit of experimental data to the second-order quadratic model. This study opens the great potential of SCW to extract algal oil for use in algal biofuel production.
Fulltext Optimization of Subcritical Water Extraction (SWE) of Lipid and Eicosapentaenoic Acid (EPA) from Nannochloropsis gaditana

Ho BCH, Kamal SMM, Danquah MK, Harun R

Biomed Res Int, 2018;2018:8273581.
PMID: 30775380 DOI: 10.1155/2018/8273581

Microalgae are a promising source of omega-3. The purpose of this study was to extract lipid with a relatively high content of eicosapentaenoic acid (EPA) from Nannochloropsis gaditana using subcritical water extraction (SWE). The effects of different temperatures (156.1-273.9°C), extraction times (6.6-23.4 minutes), and biomass loadings (33-117 g algae/L) on the extraction yield were studied. From the optimization study using central composite design (CCD), quadratic models generated for lipid yield and EPA composition were considered to be significant models (p < 0.05). The predictive equations were also formed for lipid yield and EPA composition. The predicted optimum lipid yield and EPA composition at 236.54°C, 13.95 minutes, and 60.50 g algae/L were 18.278 wt% of total biomass and 14.036 wt% of total fatty acid methyl ester (FAME), respectively.
Fulltext Subcritical Water Technology for Enhanced Extraction of Biochemical Compounds from Chlorella vulgaris

Awaluddin SA, Thiruvenkadam S, Izhar S, Hiroyuki Y, Danquah MK, Harun R

Biomed Res Int, 2016;2016:5816974.
PMID: 27366748 DOI: 10.1155/2016/5816974

Subcritical water extraction (SWE) technology has been used for the extraction of active compounds from different biomass materials with low process cost, mild operating conditions, short process times, and environmental sustainability. With the limited application of the technology to microalgal biomass, this work investigates parametrically the potential of subcritical water for high-yield extraction of biochemicals such as carbohydrates and proteins from microalgal biomass. The SWE process was optimized using central composite design (CCD) under varying process conditions of temperature (180-374°C), extraction time (1-20 min), biomass particulate size (38-250 μm), and microalgal biomass loading (5-40 wt.%). Chlorella vulgaris used in this study shows high volatile matter (83.5 wt.%) and carbon content (47.11 wt.%), giving advantage as a feedstock for biofuel production. The results showed maximum total carbohydrate content and protein yields of 14.2 g/100 g and 31.2 g/100 g, respectively, achieved under the process conditions of 277°C, 5% of microalgal biomass loading, and 5 min extraction time. Statistical analysis revealed that, of all the parameters investigated, temperature is the most critical during SWE of microalgal biomass for protein and carbohydrate production.
Fulltext Microwave-Assisted Brine Extraction for Enhancement of the Quantity and Quality of Lipid Production from Microalgae Nannochloropsis sp

Zghaibi N, Omar R, Kamal SMM, Biak DRA, Harun R

Molecules, 2019 Oct 04;24(19).
PMID: 31590304 DOI: 10.3390/molecules24193581

Toward attaining a sustainability and eco-friendly process, a green and low-cost solvent-brine (NaCl solution) is proposed, as microwave-assisted extraction (MAE) technique solvent to extract lipids from microalgae Nannochloropsis sp. The effect of NaCl concentration on the quantity and quality of the extracted lipid was assessed, while MAE parameters were optimized using response surface methodology (RSM). The content of fatty acid methyl esters (FAMEs) in the lipid was analyzed by using a gas chromatography-flame ionization detector (GC/FID). The highest lipid yield (16.1%) was obtained using 10% (w/v) brine at optimum extraction parameters of 5% (w/v) solid loading, 100 °C, and 30 min. The lipid extraction yield via optimized MAE-brine technique was thrice better than that Soxhlet extraction did and only 2% less than Bligh and Dyer (B&D) lipid extraction, which utilized harmful solvents. The proposed MAE-brine technique offered better quality lipids containing the highest amount of polyunsaturated fatty acids (PUFA) (44.5%) and omega-3 fatty acids (FAs) (43%). Hence, the MAE-brine solvent technique appears to be a promising extraction method for cheaper, greener, and faster extraction of a high-quality lipid for specialty food applications.
Fulltext Kinetics Study of Microwave-Assisted Brine Extraction of Lipid from the Microalgae Nannochloropsis sp

Zghaibi N, Omar R, Kamal SMM, Biak DRA, Harun R

Molecules, 2020 Feb 12;25(4).
PMID: 32059440 DOI: 10.3390/molecules25040784

The kinetics of lipid extraction utilizing microwave-assisted extraction (MAE) from Nannochloropsis sp. microalgae were studied using a low cost and green solvent, namely brine (NaCl) solution. The kinetic modelling of the lipid extraction was performed to evaluate the mechanism of the lipid mass transfer using different extraction models, including Fick's Law, First and Second-order Rate Law and the Patricelli mathematical model. The Patricelli mathematical model described the kinetics of lipid extraction well, with the highest average values of determination coefficient (R2 ≥ 0.952) and the lowest average values of mean relative percentage deviation (MRPD ≤ 8.666%). The lipid analysis indicated a positive influence of the microwave temperature and time on the quantity and quality of extracted lipids. SEM analysis of spent microalgae clearly shows an increase in the distorted cell with increase microwave temperature and time, which could be directly correlated to the mechanism of the MAE-brine technique.
Filshie Clip sterilization trial in Malaysia

Arshat H, Puraviappan AP, Thambu J, Ali J, Harun R

Malays J Reprod Health, 1984 Jun;2(1):14-9.
PMID: 12267516
Fulltext NFIX as a Master Regulator for Lung Cancer Progression

Rahman NIA, Abdul Murad NA, Mollah MM, Jamal R, Harun R

Front Pharmacol, 2017;8:540.
PMID: 28871224 DOI: 10.3389/fphar.2017.00540

About 40% of lung cancer cases globally are diagnosed at the advanced stage. Lung cancer has a high mortality and overall survival in stage I disease is only 70%. This study was aimed at finding a candidate of transcription regulator that initiates the mechanism for metastasis by integrating computational and functional studies. The genes involved in lung cancer were retrieved using in silico software. 10 kb promoter sequences upstream were scanned for the master regulator. Transient transfection of shRNA NFIXs were conducted against A549 and NCI-H1299 cell lines. qRT-PCR and functional assays for cell proliferation, migration and invasion were carried out to validate the involvement of NFIX in metastasis. Genome-wide gene expression microarray using a HumanHT-12v4.0 Expression BeadChip Kit was performed to identify differentially expressed genes and construct a new regulatory network. The in silico analysis identified NFIX as a master regulator and is strongly associated with 17 genes involved in the migration and invasion pathways including IL6ST, TIMP1 and ITGB1. Silencing of NFIX showed reduced expression of IL6ST, TIMP1 and ITGB1 as well as the cellular proliferation, migration and invasion processes. The data was integrated with the in silico analyses to find the differentially expressed genes. Microarray analysis showed that 18 genes were expressed differentially in both cell lines after statistical analyses integration between t-test, LIMMA and ANOVA with Benjamini-Hochberg adjustment at p-value < 0.05. A transcriptional regulatory network was created using all 18 genes, the existing regulated genes including the new genes PTCH1, NFAT5 and GGCX that were found highly associated with NFIX, the master regulator of metastasis. This study suggests that NFIX is a promising target for therapeutic intervention that is expected to inhibit metastatic recurrence and improve survival rate.
Fulltext ZFP36L2 silencing increases sensitivity to Temolozomide via G2M cell cycle arrest and BAX mediated apoptosis

Che Mat M. F., Mohamad Hanif E. A., Abdul Murad N. A., Ibrahim K., Harun R.

Malaysian Journal of Medicine and Health Sciences, 2019;15(102):11-11.
MyJurnal

Introduction: The mortality rate of glioma patients particularly with glioblastoma multiforme (GBM) remains high even with advancements in the multimodality treatment. This is partly due to chemoresistance of the glioma cells towards drug treatment which finally reduced the survival of GBM patients. In this study, we determined the chemosensitisation and oncogenic characteristics of ZFP36L2 in LN18 GBM cells using RNA interference (RNAi). Methods: Meta-analysis of microarray datasets was used to identify the druggable genes responsive to GBM chemosensitivity. Subsequently, the genes were validated using RNAi screening [pooled small interference RNA (siRNA)]. Temozolomide- resistant LN18 cells were used to evaluate the effects of gene silencing on chemosensitisation to the sub-lethal dose (1/10 of IC50) of temozolomide. Assays such as cell viability, proliferation, migration and invasion and apoptosis assays were carried out. The apoptosis pathway underlying chemosensitisation by ZFP36L2 siRNA was determined using a human apoptosis array kit. Statistical analyses were performed using one-way analysis of variance. Results: ZFP36L2 was identified as a potential marker of GBM based on the meta-analysis and RNAi screening. ZFP36L2 knockdown lead to 1) Apoptosis induction (p < 0.05) 2) Reduced cell migration (p < 0.05) 3) Reduced up to 82% of cell invasion (p < 0.01) and 4) Decreased cellular proliferation in siZFP36L2-treated LN18 cells. Downstream analysis showed that the sub-lethal dose of temozolomide caused major upregulation of BCL2-associated X, apoptosis regulator (BAX). Conclusion: ZFP36L2 is oncogenic and chemosensitive thus may contribute to gliomagenesis through cell proliferation, migration, invasion and apoptosis. RNAi therapy in combination with chemotherapy treatment such as temozolomide may serve as potential therapeutic approach in the future.
Fulltext Comparison between Ventriculosubgaleal Shunt and Extraventricular Drainage to Treat Acute Hydrocephalus in Adults

Nee LS, Harun R, Sellamuthu P, Idris Z

Asian J Neurosurg, 2017 Oct-Dec;12(4):659-663.
PMID: 29114279 DOI: 10.4103/ajns.AJNS_122_16

Context: Hydrocephalus, due to subarachnoid or intraventricular hemorrhage (IVH), meningitis, or tumor compression, is usually transient and may resolve after treatment. There are several temporary methods of cerebrospinal fluid (CSF) diversion, none of it is superior to the other, and the decision is based on its various etiologies and factors. Ventriculosubgaleal shunt (VSGS) is one of those temporary measures, which is a simple and rapid CSF decompression method without causing electrolyte and nutritional losses.

Aims: The aim is to study the efficacy of VSGS for temporary CSF diversion, compared to extraventricular drainage (EVD) in adult hydrocephalus patients; to evaluate the outcome in terms of avoiding a permanent shunt, and to look for incidences of their complications.

Settings and Design: This was a retrospective observational study.

Subjects and Methods: The data were acquired from case notes of fifty patients with acute hydrocephalus: 26 secondary to IVH, 10 from aneurysm rupture, 8 posttrauma, and 6 from infection. All these patients had undergone CSF diversion in Hospital Queen Elizabeth II, Sabah, Malaysia, between 2013 and 2015. The patients were followed up from the date of treatment until the resolution of hydrocephalus, where parameters such as shunt dependency and complications were documented.

Statistical Analysis Used: All analyses were carried out using Statistical Packages for the Social Sciences Version 22.0. Chi-squared test or Fisher's exact test is used for univariate analysis of categorical variables.

Results: A total of 21 (42%) patients underwent EVD insertion and 29 (58%) underwent VSGS insertion. Thirty-seven (74%) patients did not require a permanent shunt; 24 (64.8%) of them were from the VSGS group (P = 0.097). EVD had more intracranial complications (44.1%) compared with VSGS (23.5%), with a statistically significant P = 0.026.

Conclusions: VSGS is a safe and viable option for adult hydrocephalus patients, with the possibility of continuation of the treatment for such patients in nonneurosurgical centers, as opposed to patients with EVDs. Furthermore, even though this method had no statistical difference in avoiding a permanent ventriculoperitoneal shunt, VSGS has statistically significant less intracranial complications compared with EVD.
Fulltext Integrated analysis of copy number variation and genome-wide expression profiling in colorectal cancer tissues

Ali Hassan NZ, Mokhtar NM, Kok Sin T, Mohamed Rose I, Sagap I, Harun R, et al.

PLoS One, 2014;9(4):e92553.
PMID: 24694993 DOI: 10.1371/journal.pone.0092553

Integrative analyses of multiple genomic datasets for selected samples can provide better insight into the overall data and can enhance our knowledge of cancer. The objective of this study was to elucidate the association between copy number variation (CNV) and gene expression in colorectal cancer (CRC) samples and their corresponding non-cancerous tissues. Sixty-four paired CRC samples from the same patients were subjected to CNV profiling using the Illumina HumanOmni1-Quad assay, and validation was performed using multiplex ligation probe amplification method. Genome-wide expression profiling was performed on 15 paired samples from the same group of patients using the Affymetrix Human Gene 1.0 ST array. Significant genes obtained from both array results were then overlapped. To identify molecular pathways, the data were mapped to the KEGG database. Whole genome CNV analysis that compared primary tumor and non-cancerous epithelium revealed gains in 1638 genes and losses in 36 genes. Significant gains were mostly found in chromosome 20 at position 20q12 with a frequency of 45.31% in tumor samples. Examples of genes that were associated at this cytoband were PTPRT, EMILIN3 and CHD6. The highest number of losses was detected at chromosome 8, position 8p23.2 with 17.19% occurrence in all tumor samples. Among the genes found at this cytoband were CSMD1 and DLC1. Genome-wide expression profiling showed 709 genes to be up-regulated and 699 genes to be down-regulated in CRC compared to non-cancerous samples. Integration of these two datasets identified 56 overlapping genes, which were located in chromosomes 8, 20 and 22. MLPA confirmed that the CRC samples had the highest gains in chromosome 20 compared to the reference samples. Interpretation of the CNV data in the context of the transcriptome via integrative analyses may provide more in-depth knowledge of the genomic landscape of CRC.
MicroRNAs and Lymph Node Metastasis in Papillary Thyroid Cancers

Mutalib NS, Yusof AM, Mokhtar NM, Harun R, Muhammad R, Jamal R

Asian Pac J Cancer Prev, 2016;17(1):25-35.
PMID: 26838219

Lymph node metastasis (LNM) in papillary thyroid cancer (PTC) has been shown to be associated with increased risk of locoregional recurrence, poor prognosis and decreased survival, especially in older patients. Hence, there is a need for a reliable biomarker for the prediction of LNM in this cancer. MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene translation or degradation and play key roles in numerous cellular functions including cell-cycle regulation, differentiation, apoptosis, invasion and migration. Various studies have demonstrated deregulation of miRNA levels in many diseases including cancers. While a large number of miRNAs have been identified from PTCs using various means, association of miRNAs with LNM in such cases is still controversial. Furthermore, studies linking most of the identified miRNAs to the mechanism of LNM have not been well documented. The aim of this review is to update readers on the current knowledge of miRNAs in relation to LNM in PTC.
Fulltext Identification of diagnostic markers in colorectal cancer via integrative epigenomics and genomics data

Kok-Sin T, Mokhtar NM, Ali Hassan NZ, Sagap I, Mohamed Rose I, Harun R, et al.

Oncol Rep, 2015 Jul;34(1):22-32.
PMID: 25997610 DOI: 10.3892/or.2015.3993

Apart from genetic mutations, epigenetic alteration is a common phenomenon that contributes to neoplastic transformation in colorectal cancer. Transcriptional silencing of tumor-suppressor genes without changes in the DNA sequence is explained by the existence of promoter hypermethylation. To test this hypothesis, we integrated the epigenome and transcriptome data from a similar set of colorectal tissue samples. Methylation profiling was performed using the Illumina InfiniumHumanMethylation27 BeadChip on 55 paired cancer and adjacent normal epithelial cells. Fifteen of the 55 paired tissues were used for gene expression profiling using the Affymetrix GeneChip Human Gene 1.0 ST array. Validation was carried out on 150 colorectal tissues using the methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) technique. PCA and supervised hierarchical clustering in the two microarray datasets showed good separation between cancer and normal samples. Significant genes from the two analyses were obtained based on a ≥2-fold change and a false discovery rate (FDR) p-value of <0.05. We identified 1,081 differentially hypermethylated CpG sites and 36 hypomethylated CpG sites. We also found 709 upregulated and 699 downregulated genes from the gene expression profiling. A comparison of the two datasets revealed 32 overlapping genes with 27 being hypermethylated with downregulated expression and 4 hypermethylated with upregulated expression. One gene was found to be hypomethylated and downregulated. The most enriched molecular pathway identified was cell adhesion molecules that involved 4 overlapped genes, JAM2, NCAM1, ITGA8 and CNTN1. In the present study, we successfully identified a group of genes that showed methylation and gene expression changes in well-defined colorectal cancer tissues with high purity. The integrated analysis gives additional insight regarding the regulation of colorectal cancer-associated genes and their underlying mechanisms that contribute to colorectal carcinogenesis.
Fulltext Knockdown of Tousled‑like kinase 1 inhibits survival of glioblastoma multiforme cells

Ibrahim K, Abdul Murad NA, Harun R, Jamal R

Int J Mol Med, 2020 Aug;46(2):685-699.
PMID: 32468002 DOI: 10.3892/ijmm.2020.4619

Glioblastoma multiforme (GBM) is an aggressive type of brain tumour that commonly exhibits resistance to treatment. The tumour is highly heterogenous and complex kinomic alterations have been reported leading to dysregulation of signalling pathways. The present study aimed to investigate the novel kinome pathways and to identify potential therapeutic targets in GBM. Meta‑analysis using Oncomine identified 113 upregulated kinases in GBM. RNAi screening was performed on identified kinases using ON‑TARGETplus siRNA library on LN18 and U87MG. Tousled‑like kinase 1 (TLK1), which is a serine/threonine kinase was identified as a potential hit. In vitro functional validation was performed as the role of TLK1 in GBM is unknown. TLK1 knockdown in GBM cells significantly decreased cell viability, clonogenicity, proliferation and induced apoptosis. TLK1 knockdown also chemosensitised the GBM cells to the sublethal dose of temozolomide. The downstream pathways of TLK1 were examined using microarray analysis, which identified the involvement of DNA replication, cell cycle and focal adhesion signalling pathways. In vivo validation of the subcutaneous xenografts of stably transfected sh‑TLK1 U87MG cells demonstrated significantly decreased tumour growth in female BALB/c nude mice. Together, these results suggested that TLK1 may serve a role in GBM survival and may serve as a potential target for glioma.
Exploring breast carcinogenesis through integrative genomics and epigenomics analyses

Minning C, Mokhtar NM, Abdullah N, Muhammad R, Emran NA, Ali SA, et al.

Int J Oncol, 2014 Nov;45(5):1959-68.
PMID: 25175708 DOI: 10.3892/ijo.2014.2625

There have been many DNA methylation studies on breast cancer which showed various methylation patterns involving tumour suppressor genes and oncogenes but only a few of those studies link the methylation data with gene expression. More data are required especially from the Asian region and to analyse how the epigenome data correlate with the transcriptome. DNA methylation profiling was carried out on 76 fresh frozen primary breast tumour tissues and 25 adjacent non-cancerous breast tissues using the Illumina Infinium(®) HumanMethylation27 BeadChip. Validation of methylation results was performed on 7 genes using either MS-MLPA or MS-qPCR. Gene expression profiling was done on 15 breast tumours and 5 adjacent non-cancerous breast tissues using the Affymetrix GeneChip(®) Human Gene 1.0 ST array. The overlapping genes between DNA methylation and gene expression datasets were further mapped to the KEGG database to identify the molecular pathways that linked these genes together. Supervised hierarchical cluster analysis revealed 1,389 hypermethylated CpG sites and 22 hypomethylated CpG sites in cancer compared to the normal samples. Gene expression microarray analysis using a fold-change of at least 1.5 and a false discovery rate (FDR) at p>0.05 identified 404 upregulated and 463 downregulated genes in cancer samples. Integration of both datasets identified 51 genes with hypermethylation with low expression (negative association) and 13 genes with hypermethylation with high expression (positive association). Most of the overlapping genes belong to the focal adhesion and extracellular matrix-receptor interaction that play important roles in breast carcinogenesis. The present study displayed the value of using multiple datasets in the same set of tissues and how the integrative analysis can create a list of well-focused genes as well as to show the correlation between epigenetic changes and gene expression. These gene signatures can help us understand the epigenetic regulation of gene expression and could be potential targets for therapeutic intervention in the future.
Silencing of PROS1 induces apoptosis and inhibits migration and invasion of glioblastoma multiforme cells

Che Mat MF, Abdul Murad NA, Ibrahim K, Mohd Mokhtar N, Wan Ngah WZ, Harun R, et al.

Int J Oncol, 2016 Dec;49(6):2359-2366.
PMID: 27840905 DOI: 10.3892/ijo.2016.3755

Glioblastoma multiforme (GBM) is an aggressive brain tumor and most patients have poor prognosis. Despite many advances in research, there has been no significant improvement in the patient survival rate. New molecular therapies are being studied and RNA interference (RNAi) therapy is one of the promising approaches to improve prognosis and increase survival in patients with GBM. We performed a meta‑analysis of five different microarray datasets and identified 460 significantly upregulated genes in GBM. Loss‑of‑function screening of these upregulated genes using LN18 cells was performed to identify the significant target genes for glioma. Further investigations were performed using siRNA in LN18 cells and various functional assays were carried out on the selected candidate gene to understand further its role in GBM. We identified PROS1 as a candidate gene for GBM from the meta‑analysis and RNAi screening. Knockdown of PROS1 in LN18 cells significantly induced apoptosis compared to siPROS1‑untreated cells (p<0.05). Migration in cells treated with siPROS1 was reduced significantly (p<0.05) and this was confirmed with wound-healing assay. PROS1 knockdown showed substantial reduction in cell invasion up to 82% (p<0.01). In addition, inhibition of PROS1 leads to decrease in cellular proliferation by 18%. Knockdown of PROS1 in LN18 cells caused activation of both of the extrinsic and intrinsic apoptotic pathways. It caused major upregulation of FasL which is important for death receptor signaling activation and also downregulation of GAS6 and other members of TAM family of receptors. PROS1 may play an important role in the development of GBM through cellular proliferation, migration and invasion as well as apoptosis. Targeting PROS1 in GBM could be a novel therapeutic strategy in GBM treatment.

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