Sarina Sulong

The V617F mutation in Jak2 is not found in childhood acute lymphoblastic leukaemia

Members of the Jak kinase family, including Tyk2, Jak1, Jak2 and Jak3, play an important role in mediating cellular signals between cytokine/hormone receptors and downstream effector proteins by virtue of their tyrosine phosphorylation activities. They share structural homology and have two kinase domains, JH1 and JH2. While only the JH1 domain has kinase functionality, JH2 plays an important negative-regulatory role on JH1 activity. Recently a somatic, gain of function, mutation has been identified in JAK2 in a range of Philadelphia chromosomenegative myeloproliferative diseases including polycythaemia vera, essential thrombocythaemia and chronic idiopathic myelofibrosis (Baxter et al, 2005; Kralovics et al, 2005; Levine et al, 2005). A pointmutation in exon 12 of the JAK2 gene results in substitution of valine for phenylalanine at amino acid position 617 in the JH2 domain, leading to constitutive tyrosine phosphorylation activity and cytokine hypersensitivity. Neoplastic cells can be heterozygous for themutation or hemizygous if they are associated with loss of heterozygosity (LOH) of 9p, where JAK2 is situated. The explanation for V617F yielding different chronic myeloproliferative disease phenotypes is not clear but may relate to the target cell for transformation or the presence of other co-operating genetic events. Jak2 activation is also implicated in the pathology of childhood acute lymphoblastic leukaemia (ALL). Two studies showed constitutive activation of Jak2 in both primary samples and leukaemic cell lines, with inhibition blocking leukaemic cell growth selectively, in vitro and in vivo, by inducing programmed cell death (Meydan et al, 1996). In addition, LOH of 9p is a relatively common event, with JAK2 invariably being present in the minimally deleted region. One known mechanism of JAK2 activation in ALL is chromosomal translocation with the t(9;12)(p24;p13) yielding a chimaeric Tel–Jak2 fusion protein that has deregulated Jak2 kinase activity, confers cytokine-independent proliferation and results in the formation of ALL in a mouse model system (Lacronique et al, 1997; Peeters et al, 1997; Carron et al, 2000). However, this is a rare occurrence. Taken together, these observations provide a rationale for investigating the presence of V617F in childhood ALL. To detect the V617 mutation, we performed allele-specific polymerase chain reaction using genomic DNA isolated from bone marrow samples from children with ALL treated at our institution (Baxter et al, 2005). Eighty-six samples were collected during diagnosis and 42 samples during relapse. All samples were collected with appropriate consent. Amplicons were size fractioned by standard agarose gel electrophoresis. DNA from HEL92.1.7, an erythroleukaemic cell line, served as a positive control. None of the 128 ALL samples examined were positive for the 203-bp product, indicative of V617F mutation, but all were positive for the internal control (representative gel shown in Fig 1). Using HEL92.1.7 cells spiked into normal peripheral blood, the sensitivity of the assay was determined to be between 1% and 5%. Thus the V617F mutation is absent in childhood ALL and this finding concords with a mutational screening study of the JH2 domain in a small cohort of ALL patients (Cools et al, 1999). Given the importance of the Jak2 activation in primary ALL, a comprehensive mutational screen of all of its coding exons is warranted.

HOXA4 Gene Promoter Hypermethylation as an Epigenetic Mechanism Mediating Resistance to Imatinib Mesylate in Chronic Myeloid Leukemia Patients

Development of resistance to imatinib mesylate (IM) in chronic myeloid leukemia (CML) patients has emerged as a significant clinical problem. The observation that increased epigenetic silencing of potential tumor suppressor genes correlates with disease progression in some CML patients treated with IM suggests a relationship between epigenetic silencing and resistance development. We hypothesize that promoter hypermethylation of HOXA4 could be an epigenetic mechanism mediating IM resistance in CML patients. Thus a study was undertaken to investigate the promoter hypermethylation status of HOXA4 in CML patients on IM treatment and to determine its role in mediating resistance to IM. Genomic DNA was extracted from peripheral blood samples of 95 CML patients (38 good responders and 57 resistant) and 12 normal controls. All samples were bisulfite treated and analysed by methylation-specific high-resolution melt analysis. Compared to the good responders, the HOXA4 hypermethylation level was significantly higher (P = 0.002) in IM-resistant CML patients. On comparing the risk, HOXA4 hypermethylation was associated with a higher risk for IM resistance (OR 4.658; 95% CI, 1.673–12.971; P = 0.003). Thus, it is reasonable to suggest that promoter hypermethylation of HOXA4 gene could be an epigenetic mechanism mediating IM resistance in CML patients.

Molecular Genetic Analysis of Anaplastic Pleomorphic Xanthoastrocytoma

A case of pleomorphic xanthoastrocytoma in a 10-year-old Malay boy is reported. The patient presented with headache and epilepsy. On computed tomography, a ring-enhancing low-density lesion was observed in the left fronto-temporal area. During surgery, a cystic tumour containing serous fluid was found and almost totally removed. Histologically, the tumour exhibited marked pleomorphism of oval and spindle-shaped cells intermixed with uni- and multinucleated giant cells, and xanthomatous cells with foamy cytoplasm. The tumour displayed pericellular reticulin and periodic acid-Schiff positive granules. Focally, six mitotic characters per 10 high-power fields were seen, and necrosis was confined only to the inner lining of the cyst. Mutational analysis showed that a frameshift mutation (a 4-bp deletion) in the p53 gene had occurred in codons 273 and 274 of exon 8. No mutation was detected in the p16 gene. No allelic loss and/or loss of heterozygosity were observed on chromosome 10 using microsatellite marker D105532. The patient was treated with postoperative radiotherapy because of histological anaplasia and the presence of residual tumour. The patient showed marked neurological recovery after a follow-up period of 2 years.

Mutation Spectrum of Dystrophin Gene in Malaysian Patients with Duchenne/Becker Muscular Dystrophy

Abstract We undertook the clinical feature examination and dystrophin analysis using multiplex ligation-dependent probe amplification (MLPA) and direct DNA sequencing of selected exons in a cohort of 35 Malaysian Duchenne/Becker muscular dystrophy (DMD/BMD) patients. We found 27 patients with deletions of one or more exons, 2 patients with one exon duplication, 2 patients with nucleotide deletion, and 4 patients with nonsense mutations (including 1 patient with two nonsense mutations in the same exon). Although most cases showed compliance to the reading frame rule, we found two unrelated DMD patients with an in-frame deletion of the gene. Two novel mutations have been detected in the Dystrophin gene and our results were compatible with other studies where the majority of the mutations (62.8%) are located in the distal hotspot. However, the frequency of the mutations in our patient varied as compared with those found in other populations.

Low Level of TERC Gene Amplification between Chronic Myeloid Leukaemia Patients Resistant and Respond to Imatinib Mesylate Treatment

The amplification of telomerase component (TERC) gene could play an important role in generation and treatment of haematological malignancies. This present study was aimed to investigate copy number amplification status of TERC gene in chronic myeloid leukaemia (CML) patients who were being treated with imatinib mesylate (IM). Genomic DNA was extracted from peripheral blood of CML-IM Resistant (n=63), CML-IM Respond (n=63) and healthy individuals (n=30). TERC gene copy number predicted (CNP) and copy number calculated (CNC) were determined based on Taqman® Copy Number Assay. Fluorescence in situ hybridization (FISH) analysis was performed to confirm the normal signal pattern in C4 (calibrator) for TERC gene. Nine of CML patients showed TERC gene amplification (CNP=3), others had 2 CNP. A total of 17 CML patients expressed CNC>2.31 and the rest had 2.31>CNC>1.5. TERC gene CNP value in healthy individuals was 2 and their CNC value showed in range 1.59-2.31. The average CNC TERC gene copy number was 2.07, 1.99 and 1.94 in CML- IM Resistant patients, CML-IM Respond and healthy groups, respectively. No significant difference of TERC gene amplification observed between CML-IM Resistant and CML-IM Respond patients. Low levels of TERC gene amplification might not have a huge impact in haematological disorders especially in terms of resistance towards IM treatment.

Discovery of candidate genes for nonsyndromic cleft lip palate through genome-wide linkage analysis of large extended families in the Malay population

BackgroundNonsyndromic orofacial clefts are one of the most common birth defects worldwide. It occurs as a result of genetic or environmental factors. This study investigates the genetic contribution to nonsyndromic cleft lip and/or palate through the analysis of family pedigrees. Candidate genes associated with the condition were identified from large extended families from the Malay population.ResultsA significant nonparametric linkage (NPL) score was detected in family 100. Other suggestive NPL and logarithm of the odds (LOD) scores were attained from families 50, 58, 99 and 100 under autosomal recessive mode. Heterogeneity LOD (HLOD) score ≥ 1 was determined for all families, confirming genetic heterogeneity of the population and indicating that a proportion of families might be linked to each other. Several candidate genes in linkage intervals were determined; LPHN2 at 1p31, SATB2 at 2q33.1-q35, PVRL3 at 3q13.3, COL21A1 at 6p12.1, FOXP2 at 7q22.3-q33, FOXG1 and HECTD1 at 14q12 and TOX3 at 16q12.1.ConclusionsWe have identified several novel and known candidate genes for nonsyndromic cleft lip and/or palate through genome-wide linkage analysis. Further analysis of the involvement of these genes in the condition will shed light on the disease mechanism. Comprehensive genetic testing of the candidate genes is warranted.

MicroRNAs as Potential Biomarkers in Acute Promyelocytic Leukaemia

Acute promyelocytic leukaemia (APL) is an M3 subtype of acute myeloid leukaemia (AML). This classification is based on the morphology of promyelocytic cell. The clinical characteristics of APL can be recognized by haemorrhagic episodes, a differentiation block at the promyelocytic stage, and sensitivity to the differentiation response to all-trans-retinoic acid (ATRA). Cytogenetically, APL is characterized by a balanced reciprocal translocation between chromosomes 15 and 17, which results in the production of PML/RARα fusion protein. Recent studies reported that microRNAs (miRNAs) have also been proposed to contribute to the pathogenesis of APL. miRNAs have been associated with the pathogenesis of cancer and their involvement as oncogenic and tumour suppressor activities have been identified. They are involved in various biological processes including the cell proliferation, differentiation, growth and development, metabolism, apoptosis, and haematopoiesis. The new discovery of miRNAs as possible therapeutic markers will provide new insight for the diagnosis and therapeutic entries for the treatment of APL. This review highlights the potential of miRNAs as biomarkers in APL.

Aberrant DNA methylation at HOXA4 and HOXA5 genes are associated with resistance to imatinib mesylate among chronic myeloid leukemia patients

Imatinib mesylate is a molecularly targeted tyrosine kinase inhibitor drug. It is effectively used in the treatment of chronic myeloid leukemia (CML) patients. However, development of resistance to imatinib mesylate as a result of BCR‐ABL dependent and BCR‐ABL independent mechanisms has emerged as a daunting problem in the management of CML patients. Between these mechanisms, BCR‐ABL independent mechanisms are still not robustly understood.

Linkage evidence and methylation at 2q region in nonsyndromic cleft lip and/or palate of Malay population

Introduction: Nonsyndromic cleft lip and/or palate (NSCLP) occurs as a result of multifactorial determinants, involving both genetic and environmental factors. Several candidate genes associated with NSCLP have been discovered through genetic approach, but there is paucity of studies focusing on epigenetic determinants in NSCLP. We are interested to reveal linkage evidence of SATB2 at 2q region in large-extended NSCLP families of Malay population and its methylation activity in causing cleft formation. Materials and Methods: Eight large-extended families were included in this study. Microarray analysis was carried out and genome-wide linkage was determined using GeneHunter Multipoint Linkage Analysis v2.1r5. SATB2 methylation was tested on 100 NSCLP patients by DNA sequencing. Results: Genome-wide linkage analysis has revealed significant nonparametric linkage score and suggestive logarithm of the odds (LOD) score at 2q region in family 50 and family 100. Genome-wide heterogeneity LOD score of 2.63 and α =0.122 were found in total families at 2q33.1-q35 region. Significant copy number loss (P < 0.05) in NSCLP family compared with the normal control supports the linkage evidence of SATB2 in those families with positive linkage. Epigenetic testing found SATB2 unmethylation at DNA promoter region. Discussion: Linkage evidence and significant low copy number of SATB2 in NSCLP family of Malay population confirmed that genetic factors play a major role in causing cleft defects. SATB2 unmethylation could not support the epigenetic occurrence in causing craniofacial deformities. Conclusions: Linkage evidence and significant low copy number of SATB2 in NSCLP family of Malay population confirmed that genetic factors play a major role in causing cleft defects. SATB2 unmethylation could not support the epigenetic occurrence in causing craniofacial deformities.

Analysis of the genetic structure of the Malay population: Ancestry-informative marker SNPs in the Malay of Peninsular Malaysia

Malay, the main ethnic group in Peninsular Malaysia, is represented by various sub-ethnic groups such as Melayu Banjar, Melayu Bugis, Melayu Champa, Melayu Java, Melayu Kedah Melayu Kelantan, Melayu Minang and Melayu Patani. Using data retrieved from the MyHVP (Malaysian Human Variome Project) database, a total of 135 individuals from these sub-ethnic groups were profiled using the Affymetrix GeneChip Mapping Xba 50-K single nucleotide polymorphism (SNP) array to identify SNPs that were ancestry-informative markers (AIMs) for Malays of Peninsular Malaysia. Prior to selecting the AIMs, the genetic structure of Malays was explored with reference to 11 other populations obtained from the Pan-Asian SNP Consortium database using principal component analysis (PCA) and ADMIXTURE. Iterative pruning principal component analysis (ipPCA) was further used to identify sub-groups of Malays. Subsequently, we constructed an AIMs panel for Malays using the informativeness for assignment (In) of genetic markers, and the K-nearest neighbor classifier (KNN) was used to teach the classification models. A model of 250 SNPs ranked by In, correctly classified Malay individuals with an accuracy of up to 90%. The identified panel of SNPs could be utilized as a panel of AIMs to ascertain the specific ancestry of Malays, which may be useful in disease association studies, biomedical research or forensic investigation purposes.