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Kishor Bhatia

Publications and source records attributed to Kishor Bhatia.

16 recordsLinked to original sources
PubMed2005

Childhood and adult ALL: differences in epigenetic lesions associated with cell cycle genes.

The impact of silencing tumor suppressor genes involved in cell proliferation in adult and pediatric ALL is still unknown. We analyzed methylation of the master regulators (p73, p53, Rb), CDKIs (p27, p57), and the INK4 locus (p15) in childhood ALLs and describe a relatively low frequency. Comparisons with adult ALL showed that p57 clearly differed in children (7% methylation) and adults (50% methylation). While >20% of adult ALL Ph1 chromosome-negative undergo methylation of p73, p57, and p15, only 3% of childhood ALL carried such anomalies, which is very significant when a higher fraction of pediatric patients has non-Ph1 ALL than do the adult patients. We have studied a large p57 CpG island and expression by real-time RT-PCR. We observed that 53% of childhood leukemias lacked p57 transcripts, and the overall level was 8-fold lower than in normal lymphocytes (P < 0.0001). However, no correlation with methylation was found. Thus, loss of p57 expression in the absence of methylation may be frequent in childhood ALL, suggesting that methylation is not the sole mechanism of p57 downregulation. Methylation differences in ALL may be age-related or, alternatively, reflect different pathogenesis.

Adult↗
PubMed2005

Single monochrome real-time RT-PCR assay for identification, quantification, and breakpoint cluster region determination of t(9;22) transcripts.

t(9;22) generates the BCR-ABL fusion gene, the hallmark of chronic myeloid leukemia (CML) but also found in acute lymphoblastic leukemia (ALL). Multiple chimeric transcripts translate to proteins of 190 or 210 kd and, rarely, 230 kd. CML typically carries p210 BCR-ABL while ALL is most often associated with p190. Detection and quantification of these fusion transcripts is useful in clinical management. We have exploited the unique melting profiles of these transcripts to design a new, simple, and cost-effective assay based on monochrome multiplex real-time RT-PCR for identification and quantification of each of these transcripts (b3-a2, b2-a2, and e1-a2) without further manipulation. The sensitivity of this assay was 10(-4) for e1-a2 and 10(-5) for b3-a2/b2-a2, which is appropriate for detection of minimal residual disease (MRD). Inter- and intra-assay variation was minimal. We applied this assay to assess the distribution of p190 and p210 in 260 childhood ALL samples from India. BCR-ABL was detected in 19 (7.3%), including one T-ALL. Eight patients (3.1%) demonstrated mBCR-ABL (p190) and 11 (4.2%) had MBCR-ABL (p210). Transcript levels varied markedly (up to 3000-fold) but e1-a2 were generally expressed at higher levels than b3/b2-a2 (P = 0.05). This simple real-time multiplex assay can thus be easily applied to monitor patients with ALL as well as CML.

Adolescent↗
PubMed2005

Monochrome LightCycler PCR assay for detection and quantification of five common species of Candida and Aspergillus.

Invasive fungal pathogens, especially in immunocompromised hosts, can result in life-threatening infections. Current laboratory/radiological methods for fungal identification are time-consuming and lack sensitivity and specificity. A monochrome, multiplex, real-time PCR assay for the identification and quantification of Candida albicans, Candida krusei, Candida tropicalis, Aspergillus flavus and Aspergillus fumigatus is described here. Detection of each of these fungi was specific and demonstrated 100 % concordance with biochemical/culture identification in all 60 isolates tested. Samples from 16 febrile neutropenic patients with haematological malignancies were also analysed and the utility of the assay in clinical samples was reconfirmed without false-negative results. The sensitivity of this assay was 0.1 pg fungal genomic DNA, corresponding to three cells, for C. albicans, C. krusei, C. tropicalis and A. flavus, and 0.01 pg fungal genomic DNA, i.e. less than one cell, for A. fumigatus. The analysis allows a low-cost, simple, rapid and sensitive alternative for clinical identification and quantification of these five common fungal species.

Aspergillosis↗
PubMed2005

Biomedical data integration: using XML to link clinical and research data sets.

Data integration occurs when a query proceeds through multiple data sets, thereby relating diverse data extracted from different data sources. Data integration is particularly important to biomedical researchers since data obtained from experiments on human tissue specimens have little applied value unless they can be combined with medical data (i.e., pathologic and clinical information). In the past, research data were correlated with medical data by manually retrieving, reading, assembling and abstracting patient charts, pathology reports, radiology reports and the results of special tests and procedures. Manual annotation of research data is impractical when experiments involve hundreds or thousands of tissue specimens resulting in large, complex data collections. The purpose of this paper is to review how XML (eXtensible Markup Language) provides the fundamental tools that support biomedical data integration. The article also discusses some of the most important challenges that block the widespread availability of annotated biomedical data sets.

Data Collection↗
PubMed2004

Aberrant methylation of multiple tumor suppressor genes in acute myeloid leukemia.

Hypermethylator phenotype, a propensity of tumors to incur nonrandom concurrent methylation, has been described in several tumors, including acute myeloid leukemia (AML). More recent studies identified methylation of other tumor suppressor genes, DAP-kinase and SOCS1, singly in AML. We therefore assessed the methylation status of these genes concurrently with other known targets of methylation. We used methylation-specific PCR or COBRA to determine the extent of methylation of 10 genes in 28 AML samples from Turkey. In addition to DAP-kinase and SOCS1, we included ER, p15, and E-cadherin (reported to be frequently methylated) as well as p16, GSTP1, and HIC1 (reported as rarely methylated). We also included RARbeta and p73 for which only minimal data in AML is available. All samples were methylated at least in one locus and all except one demonstrated methylation of DAP-kinase, SOCS1, p15, and/or ER. DAP-kinase is the most frequently methylated gene in both pediatric (70%) and adult AML (55%). RARbeta is methylated in 18% and p73 in 10% of AMLs. Methylation of E-cadherin and RARbeta occurs preferentially in AMLs with high methylation index (MI), while epigenetic lesions in SOCS1, DAP-kinase, and p15 appear to be independent. MI may be age-dependent, with a peak in young adults. FAB M3 demonstrated a higher extent of methylation than M2/M4. This study provides an impetus for larger studies to define if the extent and pattern of methylation in subgroups of AML are clinically relevant.

Acute Disease↗
PubMed2004

Frequent silencing of fragile histidine triad gene (FHIT) in Burkitt's lymphoma is associated with aberrant hypermethylation.

The fragile histidine triad (FHIT) gene, a potential tumor-suppressor gene, is frequently inactivated in multiple human cancers. However, the FHIT gene remains largely unexplored in Burkitt's lymphoma (BL). Hence, we assessed whether loss of FHIT expression occurs in BL, and, if so, what is the mechanism of such loss. Lack of protein expression was observed in 50% of BL cell lines. Methylation-specific polymerase chain reaction (MSP) showed that 45% of BL cell lines carried aberrantly methylated FHIT alleles. Sequencing of bisulfite-treated DNA confirmed these data and indicated a very high density of methylation in all methylated alleles. Real-time, quantitative reverse-transcription PCR analysis indicated that attenuation of full-length FHIT transcription was correlated with methylation. Sequencing of transcripts illustrated that aberrant transcription resulting in loss of FHIT exons occurred more commonly in BL containing unmethylated FHIT genes. However, such transcripts often coexisted with full-length FHIT transcripts. Not surprisingly, therefore, loss of FHIT protein in BL correlated with CpG island methylation, rather than with aberrant transcription. FHIT methylation also was detected in 31% (16 of 51) of the primary BLs examined, including 2 samples whose derived cell lines also manifested FHIT hypermethylation. Aberrant methylation can thus occur in vivo. In summary, this report provides evidence that epigenetic modification frequently results in loss of FHIT expression in BL.

Acid Anhydride Hydrolases↗
PubMed2004

Immature B cell malignancies synthesize VEGF, VEGFR-1 (Flt-1) and VEGFR-2 (KDR).

Expression of VEGF and VEGFR support a role for angiogenic pathways in the pathogenesis of some hematological malignances. Our goal was to determine if expression of these angiogenic molecules also extend to childhood precursor B cell acute lymphoblastic leukemia (pre-B ALL). We now show that transcripts of VEGF, and its receptors VEGFR-1 and VEGFR-2 are concomitantly expressed in both ALL cell lines and primary pre-B ALL. Western blot and ELISA consistently detected VEGF protein in the supernatants of the cell lines. Similarly, VEGFR-1 and VEGFR-2 proteins are also detectable by FACS analysis. Interestingly, the expression of the receptors in immature B cells is limited to the intra-cytoplasmic compartment and may suggest either internalization of the receptors or a block in trafficking of the receptor to the surface.

Autocrine Communication↗
PubMed2004

CpG island methylation in Schistosoma- and non-Schistosoma-associated bladder cancer.

Urothelial carcinomas (TCC) constitute the vast majority of bladder cancers in most of the world. On the other hand, squamous cell bladder carcinoma, a rare subtype in the Western world, is a common subtype in areas with endemic Schistosoma infection. Although schistosomal infection has been reported to influence DNA methylation, the pattern and extent of CpG island hypermethylation in squamous cell carcinomas remain unknown. In this study, we used methylation-specific PCR to characterize 12 cancer-related genes in 41 bladder cancer samples from Egypt (31 squamous cell carcinomas (SCC), 21 of them associated with Schistosoma and 10 TCC, five of which were Schistosoma-associated). The genes analyzed included E-cadherin, DAP-Kinase, O6MGMT, p14, p15, p16, FHIT, APC, RASSF1A, GSTP1, RARbeta and p73. Methylation of at least one gene was detected in all squamous cell tumors except two, and 45% of samples had at least three methylated genes. The average methylation index was 0.24, corresponding to three of the 12 analyzed genes. Schistosoma-associated tumors had more genes methylated than non-Schistosoma tumors (average MI: 0.29 vs 0.14) (P = 0.027). Although the extent of methylation in TCC (average MI: 0.16) was lower than in squamous cell carcinomas (SCC), the overall profile of methylation was similar, with Schistosoma-associated cases having a higher methylation index. Our results suggest that schistosomal involvement associates with a greater degree of epigenetic changes in the bladder epithelium.

Acid Anhydride Hydrolases↗
PubMed2004

Differences in the expression of apoptotic proteins in Burkitt's lymphoma cell lines: potential models for screening apoptosis-inducing agents.

Mammalian cells undergo programmed cell death by orchestrated interactions involving multiple independent pathways. At least one of them, the p53-dependent pathway is commonly compromised in Burkitt's lymphoma (BL) cell lines. Differences in the integrity of this pathway in various BL cell lines have made them useful experimental models in understanding response to standard or novel antitumor drugs vis-a-vis the p53 pathway. Non-p53-dependent loss of apoptotic regulation also contributes to the genesis and/or progression of lymphomas and it is possible that BL cell lines also represent these models. We have characterized the expression of multiple apoptotic proteins in a panel of BL cell lines and describe cell lines with loss of cIAP1, cIAP2, Bax, Bak, Bcl-Xs and p38 MAP-kinase. This data should make this panel of cell lines a useful screening system for testing novel apoptotic inducers.

Apoptosis↗
PubMed2004

Aberrant promoter methylation of multiple genes throughout the clinico-pathologic spectrum of B-cell neoplasia.

BACKGROUND AND OBJECTIVES: Aberrant promoter methylation targets CpG islands causing gene silencing. We explored aberrant promoter methylation of genes potentially involved in B-cell malignancies and encoding proteins implicated in DNA repair (O6-methylguanine-DNA methyltransferase, MGMT), detoxification of environmental xenobiotics (glutathione S-transferase P1, GSTP1), apoptosis regulation (death associated protein kinase, DAP-k and caspase 8, CASP8) and cell cycle control (p73). DESIGN AND METHODS: Three hundred and seventeen B-cell malignancies were investigated by methylation-specific polymerase chain reaction (MSP) of MGMT, GSTP1, DAP-k, CASP8 and p73 genes. In selected cases, MSP results were matched to protein expression studies by immunohistochemistry or Western blotting. RESULTS: DAP-k promoter methylation occurred at highest frequency in follicular lymphoma (85.0%) and MALT-lymphoma (72.2%). MGMT methylation targeted both precursor B-cell neoplasia (23.8%) and mature B-cell tumors (27.6%). GSTP1 methylation was commonest in hairy cell leukemia (75.0%), follicular lymphoma (55.5%), Burkitt s lymphoma (52.0%), and MALT lymphoma (50.0%). Methylation of p73 and CASP8 was rare or absent. DAP-k and MGMT methylation caused absent protein expression. INTERPRETATION AND CONCLUSIONS: Methylation of MGMT, DAP-k and GSTP1 represents a major pathogenetic event in several B-cell malignancies. In follicular lymphoma and MALT lymphoma, frequent inactivation of the apoptosis extrinsic pathway through DAP-k methylation may reinforce the survival advantage already conferred by deregulation of the intrinsic apoptotic pathway. Inactivation of GSTP1 in gastric MALT lymphoma represents an additional mechanism favoring accumulation of reactive oxygen species and lymphomagenesis. Finally, the frequency of GSTP1 aberrant methylation in diffuse large B-cell lymphoma prompts studies aimed at verifying the prognostic impact of this epigenetic lesion in these lymphomas.

Acyltransferases↗
PubMed2003

The tumor suppressor gene 14-3-3 sigma is commonly methylated in normal and malignant lymphoid cells.

14-3-3 sigma/Stratifin was first identified as an epithelial cell antigen (HME-1) exclusively expressed in epithelia. However, the functional role of sigma in cell proliferation and apoptosis would suggest that this protein could be relevant to the regulation of growth and differentiation of multiple cell types. Recent evidence demonstrates that sigma acts as a tumor suppressor gene that is inactivated by methylation of its 5' CpG islands in epithelial tumor cells. In normal epithelia, sigma is commonly unmethylated. The objective of this study was to determine the methylation status of sigma in lymphoid cells. We now demonstrate by methylation-specific PCR analysis that sigma is also methylated in normal and malignant lymphocytes. Such methylation, however, fails to completely silence its expression. Compared with the robust expression in epithelial cells, lymphocytes showed basal, but clearly evident, levels of sigma as determined by reverse transcription-PCR and Western blot. The finding of sigma 5' region methylation in lymphocytes has direct implications in the use of body fluids on methylation tests for noninvasive monitoring of occult epithelial tumor cells and suggests that sigma may not be an adequate biomarker for methylation-specific PCR analysis.

14-3-3 Proteins↗
PubMed2003

Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and Fas apoptosis in Burkitt's lymphomas with loss of multiple pro-apoptotic proteins.

BACKGROUND AND OBJECTIVES: Normal B-cells in the germinal center (GC) may be exposed to both tumor necrosis factor-related apoptosis inducing ligand (TRAIL) and Fas-L. Whether abrogation of TRAIL apoptosis is a feature in the genesis of B cell lymphomas of GC-phenotype is not known. We assessed the integrity of the TRAIL pathway in Fas-resistant and Fas-sensitive Burkitt s lymphomas (BLs). DESIGN AND METHODS: Expression of TRAIL receptors was determined by flow cytometry and Western blots. The extent of apoptosis following exposure to TRAIL was measured by annexin-V/propidium iodide dual staining. The integrity of the Fas and TRAIL apoptotic pathways was determined by Western blotting to assess cleavage of downstream caspases. Western blot analyses were used to determine the expression of pro- and anti-apoptotic proteins and the profile of expression was correlated with response to TRAIL and CH11. RESULTS: Our results demonstrate that BL expresses both functional and decoy TRAIL receptors. BLs with a functional Fas pathway retained sensitivity to TRAIL: Frequent and compound loss of expression of pro-apoptotic proteins can be identified in BLs resistant to Fas. However, loss of Bax, Bak and Bcl-Xs did not compromise sensitivity to TRAIL: INTERPRETATION AND CONCLUSIONS: Our results indicate that BLs frequently retain sensitivity to the TRAIL pathway. These results underscore the utility of TRAIL-based therapeutic strategies in the treatment of those B-cell lymphomas that may have compromised expression of several pro-apoptotic proteins.

Apoptosis↗
PubMed2002

Discrete alterations in the BZLF1 promoter in tumor and non-tumor-associated Epstein-Barr virus.

BACKGROUND: Although the Epstein-Barr virus (EBV) is associated with malignant and nonmalignant diseases, its lytic replication is predominantly associated with nonmalignant diseases such as acute infectious mononucleosis (IM) or chronic active EBV infection. Lytic replication is also associated with type B EBV more than with type A EBV. Sustained lytic replication, however, is not compatible with tumor growth. We investigated whether control of an EBV lytic regulatory gene, BZLF1, differed in these diseases. METHODS: Polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP) and direct DNA sequence analyses were used to characterize the promoter sequence of BZLF1 (Zp) in 52 tumors (34 non-Hodgkin's lymphomas, 13 post-transplant lymphoproliferative disease samples, and five nasopharyngeal carcinomas), and in peripheral blood lymphocytes from seven patients with chronic active EBV, six with IM, and 40 healthy, EBV-seropositive individuals. All sequences were compared with the prototype EBV strain B95.8 sequence. All statistical tests were two-sided. RESULTS: Three polymorphic Zp sequences were detected. Among the malignant samples, sequence Zp-P, associated with 84% of type A EBV, was identical to that of EBV strain B95.8, whereas a second sequence (Zp-V3), associated exclusively with type B EBV (P<.001), contained three base substitutions. Among the nonmalignant samples, a distinct polymorphism, Zp-V4, containing the substitutions detected in Zp-V3 and an additional base change, was identified in all samples from chronic active EBV, IM, and healthy individuals, but in none of the malignant samples (P<.001). Zp-V4 was independent of the EBV type. CONCLUSIONS: Polymorphisms in the regulatory sequences of BZLF1 are differentially distributed among malignant and nonmalignant cells and may identify EBV subtypes with various lytic activities, including those not associated with malignancies.

Burkitt Lymphoma↗
PubMed2002

Lymphoid neoplasms in HIV-positive individuals in India.

The HIV epidemic in the Asian subcontinent has a significant impact on India. Patients with AIDS have an increased risk of developing non-Hodgkin lymphoma (NHL). In this study, we have investigated the pattern of distribution of lymphoid neoplasms and also studied the Epstein-Barr virus (EBV)-association and p53 expression in 35 HIV-positive patients from India. The biopsy samples were studied for histology and for expression of CD20, CD3, CD15, CD30, light chains, CD138, bcl-6, epithelial membrane antigen, EBV-latent membrane protein-1, and p53 protein. In situ hybridization was performed with digoxigenin-labeled anti-sense EBV-encoded nuclear RNA-1 (EBER-1) probe. Polymerase chain reaction (PCR) was performed on DNA extracted from paraffin sections for EBV-subtype analysis. The 35 cases included 7 cases of Hodgkin disease (HD), 4 cases of plasmacytoma (PL), and 24 cases of NHL. Among the cases of NHL, 3 were Burkitt lymphoma (BL), 4 were diffuse large B-cell lymphoma (DLBL) of centroblastic type (CBL), 10 were DLBL of immunoblastic type (IBL), 4 were high-grade B-cell lymphoma (unspecified) and the rest were other subtypes. EBV-association was noted in all cases of HD, 2 of 3 BL, and 3 of 10 IBL. PCR analysis of the EBNA-3C gene revealed amplimers corresponding to type A. A p53 protein overexpression was noted in 6 of 10 IBLs, 1 of 3 BLs, 2 of 3 CBLs, and 5 of 7 cases of HD. This is the first reported study of lymphoid malignancies in HIV-positive individuals from India.

Adult↗
PubMed2002

Preclinical validation of a monochrome real-time multiplex assay for translocations in childhood acute lymphoblastic leukemia.

PURPOSE: The purpose is to develop a real-time multiplex reverse transcription-PCR assay for detection and quantification of leukemia-specific chimeric transcripts that identify the genetic subgroups of acute lymphoblastic leukemias (ALLs) proposed by the WHO classification. EXPERIMENTAL DESIGN: Real-time multiplex assay for t(12;21), t(4;11), and t(1;19) with hypoxanthine phosphoribosyltransferase as internal standard used in tandem with a new real time quantitative-RT-PCR assay for the t(9;22). This new strategy was designed to yield an amplicon from each translocation with a distinct melting peak allowing dependable identification using only Sybr green I, without any need for expensive hybridization probes. RESULTS: We validated this method with 92 primary ALLs and identified 4 E2A-PBX1, 4 mBCR-ABL and 10 TEL-AML1. When compared with conventional RT-PCRs and Southern blot analyses, 100% concordance was obtained. During the course of these studies, we found marked variations in the levels of the TEL-AML1 transcripts in individual patients. We, therefore, extended the study to accurately and reproducibly determine TEL-AML1 mRNA levels in 47 additional patients with t(12;21). The results indicated that the level of expression of TEL-AML1 varied among individual patients, and it was independent of the WBC count. CONCLUSIONS: Our new real-time multiplex assay can be used for rapid, simple, and reliable classification of pediatric ALL. Its reproducible quantification results should also facilitate studies on minimal residual disease. The observed variation in TEL-AML1 transcript levels is of interest because it could reflect biological and/or clinical heterogeneity in the behavior of these leukemias.

Blotting, Southern↗