Colorectal cancer (CRC) is an important health problem that is on the rise globally, where it is the fourth most com-mon cause of deaths from cancer. CRC is now the 2nd commonest cancer in men and 3rd commonest in women in Malaysia. Diet, lifestyle, genetics and environmental interaction, together with underlying gut conditions such as inflammatory bowel disease have been reported to contribute to the disease. In addition, the gut microbiome has also been increasingly reported to be associated with CRC development, with dysbiosis of the commensal bacteria ob-served in CRC patients. Bacterial genera such as Bacteroides, Fusobacterium and Prevotella are more commonly de-tected in CRC patients compared to healthy individuals. Nevertheless, not much is known about the gut microbiome among Malaysians with different ethnicities. In Malaysia, the Chinese has the highest incidence of CRC, followed by Malays and Indians. The reason behind this difference may be contributed by the differences in the dietary intake that could modulate the gut microbiome and contribute towards the development of CRC. The current knowledge on this field still much depends on reports from individuals of American, European, Chinese, Brazilian and Japanese descendants in origin. The oncogenic potential of bacteria was suggested to include inflammation and the produc-tion of mutagenic toxin. A significant increase in certain intestinal microbiota including the genuses Enteroccus and Streptococcus spp. was detected in the advanced stage of colorectal adenoma. However, there are discrepancies in the previous studies, where some bacteria genera might be over-reported or underestimated. It is likely that the gut microbiome differs between populations. There is also no available data on the gut microbiome of the healthy individuals, colorectal adenoma (pre-cancerous) and colorectal cancer patients in the Malaysian population. Recent advancements in next generation sequencing allow faster and more accurate determination of microbial consortium in various niches of the human body and environment. In particular, sequencing of the 16S rRNA gene with specific primers have been reported to allow accurate determination of bacterial orders commonly found in the human gut as well as for those which are not expected in the digestive system. Recent developments in gut microbiome DNA ex-traction also contributed to the robustness of gut microbiome determination and analysis. All the above will contrib-ute towards an accurate and rapid cataloging process of the Malaysian gut microbiome and also enable comparison between healthy individuals, colorectal adenoma and CRC patients of the Malaysian population.
The thalassaemias are the commonest single gene disorders amongst the inherited diseases. In Malaysia, there are an estimated 2200 transfusion dependent thalassaemia patients. With a carrier rate of 3-5%, 120-340 new cases of thalassaemia are expected to be born each year. The reference treatments for these patients are regular blood transfusions and iron chelation therapy. With optimal management, these patients are able to survive into the third or fourth decade of life and most importantly avoid the complications related to transfusions and iron overload. The use of desferal locally is still limited to only those who can afford i.e. about 30% of the cases. Treatment for some of the complications such as hepatitis C, diabetes mellitus, growth impairment and pubertal delay, are now available. Curative treatment approaches like bone marrow transplantation have now become standard treatment for eligible cases whilst cord blood transplantation may yet offer hope for those who are without compatible sibling donors. Research on globin gene therapy looks very promising but will probably take some time to deliver. Hb F switching is a very novel idea but so far the results are mainly anecdotal. Finally, the strive for optimal management of thalassaemia must come hand in hand with a prevention programme to achieve a reduction of new cases.
Precision medicine is mainly about genome-driven
clinical decision-making which is the use of genome
data from the patient to decide on tailoring the best
treatment for the patient. The completion of the human
genome project in 2003 has paved the way for a deeper
understanding of diseases at the molecular level. The
term genomics medicine has since emerged as
clinicians and researchers capitalized on the
knowledge of the genome to improve the management
of many diseases. In the past decade, the term
personalized or precision medicine was introduced to
represent the tailoring of treatment to each individual
based on a person’s unique genetic makeup,
environment and lifestyle [1]. The coining of the term
precision medicine, as opposed to the more common
term ‘personalised medicine’, was intended to
highlight the principle that subgroups of patients could
be defined, often by genomics, and given treatment in
more specific ways [2]. In simple terms, it means
giving the right treatment to the right patient at the
right time with the right outcome. The concept is not
entirely new as it has been applied before in the
practice of blood transfusion where each patient is
given the appropriate blood units based on their blood
groups. However, the emergence of genome data has
allowed a more comprehensive application of
personalized medicine to make it more precise. The
unravelling of the molecular events in certain diseases
like cancers has also led to the development of targeted
therapies. (Copied from article)
The invasion of cancer cells into the peritumoral, lymph node and perineural system could be detrimental
on cancer patients. In colorectal cancer (CRC) patients, the presence of lymphovascular (LVI) and/or
perineural (PNI) invasion could significantly influence on the survival rates, treatment options and
recurrence tendencies. To date, no study has analyzed the molecular profile of the concomitant existence of
LVI and PNI in CRC. Here, we reanalyzed The Cancer Genome Atlas (TCGA) CRC datasets and focused
on cases where the information regarding LVI and PNI are available (n=176). We performed differential
gene expression, methylation and microRNA analysis by comparing the groups having both or either LVI
and PNI with the control group (LVI negative and PNI negative). Although there was no significant
difference in the methylation and miRNA profiles, we identified a number of differentially expressed genes
(DEGs). The comparison between the LVI+PNI+ and LVI-PNI- groups revealed key DEGs including
SFTA2, PHACTR3, CRABP2, ODZ3, GRP, HAP1, CSDC2, TMEM59L and HDAC9. Meanwhile, in the
LVI-PNI+ vs LVI-PNI- group, some of the DEGs found were PTPRR, EFNA2, FGF20, IGFL4, METRN
and IGFBPL1. We believe that this study could be beneficial and add value to further understand the
complex molecular profiles of CRC.
We report a rare case of undifferentiated (embryonal) sarcoma of the liver in a six-year-old girl who at presentation, had fever, right hypochondrium pain and hepatomegaly. The diagnosis was clinched by fine needle aspiration cytology and was subsequently reconfirmed by histopathological examination of the resected tumour. Pre-operative chemotherapy was given because primary resection was deemed not possible. The patient underwent a successful extensive hepatectomy followed by continuation chemotherapy
Primary liver cancer is one of the most common cancer in the world with highest cancer mortality rate. The most common type of primary liver cancer is hepatocellular carcinoma (HCC). There are many risk factors for liver cancer and currently available treatments for HCC are largely inadequate. Gene mutation and dysfunction of p53 are common and is recognized as an important molecular event in hepatocarcinogenesis. Therefore, replacement of the aberrant p53 gene is an attractive approach in the treatment of HCC providing an alternative treatment for primary HCC. In this study, we assessed whether the transfection with wild-type p53 gene is able to restore the pro-apoptotic effects and evaluate the feasibility of gene therapy in fixing a faulty p53 molecule. We established a non-viral cationic lipid-based p53 gene delivery into two human HCC cell lines namely HLF and PLC/PRF/5 cells. Both cell lines have mutations in the p53 gene. We compared the results with the normal liver cell line, WRL68, that constitutively expresses the wild-type p53 gene. In this study, the introduction of wild-type p53 gene into HLF and PLC/PRF/5 cells resulted in an increased of p53 gene expression, protein expression and cells growth inhibition shown in MTS reduction cell viability assay, FITC-Annexin V and PI apoptosis assay, western blot and caspase activity assay. In summary, the study provides a promising therapeutic approach for p53 gene delivery into HCC patients. The p53 gene delivery can be instituted together with chemotherapy as a combination treatment to induce apoptosis.
Many studies have shown that the immune response highly depends on the inheritance of specific HLA
genes in promoting the generation of T cells for the elimination of pathogens. Loss or alteration of HLA
antigen expression in tumor cells has been observed in a variety of human malignancies leading to immune
escape or immune resistance. We investigated whether the inheritance of certain alleles of HLA class II
genes confers susceptibility or resistance towards the development of colorectal carcinoma (CRC).
Molecular typing of HLA DRB1, DQB1 and DPB1 alleles in 42 patients diagnosed with CRC and 50
ethnically matched healthy controls using the PCR-sequence based typing (PCR-SBT) was conducted. The
HLA DPB1*02:01:02 was significantly higher in CRC patients (38.1%, p=0.0189) compared to healthy
controls (16%). Also, HLA DQB1*05:02:01 was present in 28.6% of CRC patients but only 10% of healthy
controls (p=0.0278). The odds ratios for HLA DPB1*02:01:02 and HLA DQB1*05:02:01were 3.23 and 3.60,
respectively. There were no significant association observed for the DRB1 allele with CRC. Our study
suggests that the HLA DPB1*02:01:02 and HLA DQB1*05:02:01 alleles may confer a higher risk for CRC
Entero- and exfoliative toxin gene profiling of 237 methicillin-susceptible Staphylococcus aureus (MSSA) isolated
from Universiti Kebangsaan Malaysia Medical Centre (UKMMC) were carried out via PCR amplification. Among
the tested toxin genes, sei was found to be the most prevalent (54.9%).
Glioblastoma multiforme (GBM) is a high-grade brain tumor of which the survival patients remain poor.
Tousled-like kinase 1 (TLK1), a serine-threonine kinase, was identified to be overexpressed in cancers such
as GBM. TLK1 plays an important role in controlling survival pathways. To date, there is no structure
available for TLK1 as well as its inhibitors. We aimed to create a homology model of TLK1 and to identify
suitable molecular inhibitors that are likely to bind and inhibit TLK1 activity via in silico high-throughput
virtual screening (HTVS) protein-ligand docking. The 3D homology models of TLK1 were derived from
various servers. All models were evaluated using Swiss Model QMEAN server. Validation was performed
using multiple tools. Energy minimization was performed using YASARA. Subsequently, HTVS was
performed using Molegro Virtual Docker 6.0 and ligands derived from ligand.info database. Drug-like
molecules were filtered using ADME-Tox filtering program. Best homology model was obtained from the
Aurora B kinase (PDB ID:4B8M) derived from Xenopus levias structure that share sequence similarity with
human TLK1. Two compounds were identified from HTVS to be the potential inhibitors as it did not violate
the Lipinski rule of five and the CNS-based filter as a potential drug-like molecule for GBM
Childhood obesity is a global epidemic, which leads to the increasing number of studies on genetic locations associated with obesity-related traits. Polymorphisms of insulin (INS) gene have been shown to be associated with obesity-related phenotypes in Europeans; while insulin receptor (INSR) gene has been associated with energy regulation. Therefore, this study was conducted to investigate the association between the INS (rs689) and INSR (rs3745551) gene polymorphisms with childhood obesity risk in a Malay childhood population. Normal weight (538) and overweight or obese (557) children aged 6-12 years old were genotyped using semi-automated Sequenom iPLEX® Gold. Body mass index (BMI) was calculated from measured body weight and height. The rs689 (T/T: 0.006, A/T: 0.159 and A/A: 0.835) and rs3745551 (G/G: 0.054, A/G: 0.378 and A/A: 0.568) genotype distributions were consistent with Hardy Weinberg equilibrium. The T-minor allele frequency for rs689 was 8.6% and G-minor allele frequency for rs3745551 was 24.3%. Minor allele of INS gene polymorphisms significantly increased risk of obesity among Malay children (sex- and age-adjusted
OR=1.580; 95%CI: 1.134-2.201). However, INSR gene polymorphisms were not significantly associated with childhood obesity. In conclusion, the polymorphisms of INS gene, rather than INSR gene, were associated with childhood obesity in the Malay population.
Background: The HLA-B*15:02 polymorphism in epileptic patients is known to be associated with carbamazepine-induced Stevens-Johnson syndrome (SJS). The prevalence of HLA-B*15:02 polymorphism seemed to be ethnic-specific with a higher frequency of HLA-B*15:02 in Asian compared to the Europeans. This study was performed to determine the frequency of the HLA-B*15:02 polymorphism in epileptic patients at the Chancellor Tuanku Muhriz Hospital-UKM Medical Centre (HCTM-UKMMC) using high resolution melting-real time PCR (HRM-QPCR) method.
Methods: We performed a fast and effective in-house high resolution melting-real time polymerase chain reaction method and compared it with the conventional multiplex-PCR method. The specificity and sensitivity of each test were also determined using DNA from saliva.
Results: Using the conventional multiplexPCR approach for screening, 25 out of 64 (39.1%) epileptic patients were positive for HLA-B*15:02. However, using the HRM-QPCR technique, 24/64 (37.5%) of the patients were positive. The one patient who tested positive by the multiplex-PCR but negative using the HRM-QPCR turned out to be negative by DNA sequencing. The HRM-QPCR and DNA sequencing showed 100% sensitivity and specificity. The multiplex-PCR showed 100% sensitivity and 98.4% specificity compared to both HRM-QPCR and DNA sequencing. The HRM-QPCR is also more cost-effective (
We report a case of bone marrow necrosis preceding infantile acute lymphoblastic leukaemia (ALL). Bone marrow necrosis is a rare antemortem event and has been known to be present in many conditions, notably in haematological malignancies like acute lymphoblastic leukaemia. This case was a 6-month-old Chinese boy who was referred to Hospital Universiti Kebangsaan Malaysia for further investigation of pancytopaenia, high-grade fever, bloody diarrhoea and petechial rashes for one week. His first bone marrow aspirate revealed bone marrow necrosis. His clinical condition improved after ten days. However, his full blood picture then revealed the presence of 5% blast cells. His subsequent marrow 2 weeks later revealed acute lymphoblastic leukaemia (FAB-L1) and immunophenotyping showed precursor B acute lymphoblastic leukaemia-null type. He was started on United Kingdom Acute Lymphoblastic leukaemia (UK ALL) Infantile Leukaemia protocol, however, he defaulted treatment after 3 days. Mode of presentation, mechanism of disease and laboratory investigations and outline of treatment will be discussed.
VACTERL association is a rare genetic disorder involving at least three of the following congenital
malformations: vertebral defects (V), anal atresia (A), cardiac defects (C), trachea-oesophageal fistula with
or without oesophageal atresia (TE), renal anomalies (R) and limb abnormalities (L). Until now, the
aetiology of VACTERL association is unknown, particularly at the molecular level. Here, we performed
whole exome sequencing (WES) of an infant with VACTERL association. The patient was delivered
prematurely at 30 weeks and had 4/6 of the VACTERL malformations. Trio-WES analysis was performed
using Torrent Suite and ANNOVAR. Polymorphisms with an allele frequency of >0.01 were excluded, and
the remaining variants were filtered based on de novo mutations, autosomal recessive, X-linked and di-genic
inheritance traits. In this patient, no homozygous, compound heterozygous or X-linked mutations was
associated with VACTERL. However, we identified two heterozygous mutations; KIF27
(ENST00000297814: c.3004A> C:p.N1002H) and GNAS (ENST00000371098: c.205C>A:p.H69N) genes that
were inherited from her father and mother respectively. A de novo, IFT140 gene mutation
(ENST00000426508: c.683C>G:p.S228C) was also identified in this patient. The VACTERL phenotype in
this patient may due to heterozygous mutations affecting KIF27 and GNAS genes, inherited via autosomal
recessive trait. In addition, the IFT140 gene mutation may also be involved. These genes are known to be
directly or non-directly involved in the sonic hedgehog signalling that is known to be implicated in
VACTERL. This is the first report of these genetic mutations in association with VACTERL.
Glioma is the most common primary brain tumour of the central nervous system. Many genetic alterations
and mutations have been identified in glioma using various approaches. We performed DNA sequencing on
the tumours of 16 patients with Grade I, II, III and IV glioma. The AmpliSeq Cancer Primers Pool was used
to generate the amplicons. The targeted-ion sphere particles were prepared using the Ion One Touch and
Ion Enrichment systems. DNA sequencing was performed on the Ion Torrent Personal Genome Machine
(PGM) and the data were analysed using the Torrent Suite Software.
In total, 14 mutations were identified in the following genes: KDR (Q472H), MLH1 (V384D), MET (N375S),
PTPN11 (E69K), BRAF (V600E), TP53 (D149E, E154K, V157F), IDH1 (R132H), PIK3CA (H1047R), CSF1R
(c1061_1061 ins A), KIT (M541L), PTEN (c1373_1373 del A) and PDGFRA (E556V). In addition, there were
four novel mutations identified; TP53 (E154K, and D149E), CSF1R (c1061_1061 ins A) and PDGFRA
(E556V). The pathogenicity prediction showed that only three mutations were pathogenic: PTPN11 (E69K),
BRAF (V600E) and Tp53 (E154K). These mutations result in changes of the proteins’ structure and could
affect their functions. Pathway analyses suggested that these genes are closely related to the pathogenesis of
GBM through several pathways such as proliferation and invasion, metabolism and angiogenesis.
In conclusion, PGM in combination with the AmpliSeq Cancer Panel could be utilised as a potential
molecular diagnostic tool not only for glioma but also for other cancers.
Nor Azian Abdul Murad, Sue-Mian, Then, Mohd Ridhwan Abdul Razak, Conjeevaram, Rajendrarao Thambidorai, Sri Noraima Othman, Rosniza Mohamad Hussain, et al.
Hirschsprung’s disease (HSCR) is a disorder associated with congenital absence of ganglion cells in the
gastrointestinal tract. Molecular analyses have identified variants in various genes including RET, GDNF,
EDN3 and EDNRB that are involved in the development, migration and survival of neural cells. Variants
in the receptor tyrosine kinase (RET) are most common and have been identified in 10-20% of sporadic
HSCR patients. The objective of this study was to screen for RET gene variants in Malaysian patients with
HSCR. Thirty-two patients with HSCR and 30 normal controls were recruited for this study. Mutations
were screened using the Polymerase Chain Reaction – Denaturing High Performance Liquid
Chromatography (PCR-dHPLC) approach. Mutations identified were then confirmed using Sanger
sequencing. We identified one novel rare variant in exon 4 (A268A c807 G>C) in one patient. We also
identified the common coding sequence variantsA45A (c135G>A), A432A (c1296A>G), L769L (c2307 T>G)
and the G691S in our cohort of patients. In conclusion, our Malaysian patients with HSCR diseases showed
the presence of similar RET gene common variants which have been described in other populations. We
have also identified a novel variant in exon 4 (A268A).
This study aimed to assess the physical activity levels of pediatric patients with acute leukemia undergoing chemotherapy. Thirty-eight pediatric patients and matched controls, aged 3-12 years old, were measured for weight, height, and other anthropometric parameters. Physical activity was assessed using actical accelerometer and activity log book. Patients recorded significantly lower mean total activity counts (26.2±30.2 cpm vs. 192.2±68.8 cpm; p<0.01) and spent more time in sedentary activities (1301±121 min vs. 1020±101 min; p<0.001) compared to controls. They also achieved fewer 1-5-min bouts of moderate-vigorous physical activity (MVPA) compared to controls (1.50±5.95 vs. 37.38±40.36; p<0.001). In conclusion, patients had lower physical activity level and intensity; and simple exercise intervention programs may be needed to minimize the detrimental effects of prolonged sedentary behaviors.