A Chakraborti

Biomedical Informatics Centre, Chandigarh, Chandīgarh, India

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Publications (47)92.68 Total impact

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    ABSTRACT: Nontypeable Haemophilus influenzae (NTHi) is an important cause of lower respiratory tract infections, resulting in exacerbations of chronic obstructive pulmonary disease (COPD). Despite its pathogenic potential, little is known regarding role of intracellular NTHi in pathogenesis of pulmonary infection. Kinetics of NTHi internalization was studied using gentamicin protection assays. NTHi strains isolated from COPD patients efficiently adhere to and invade type II alveolar (A549) cells. During early stages i.e. 6h postinfection, we noted substantial increase in NTHi invasion with no evidence of intracellular replication. Electron microscopy revealed that majority of internalized NTHi resided within membrane bound acidic endocytic vacuoles. However, at later stages i.e. 8h postinfection significant reduction in viable intracellular NTHi was observed and vacuoles were found to be empty with NTHi escape into the cytosol. By 12h, cytopathic changes of cells were evident with massive vacuolization of cytoplasm, intense chromatin condensation and intact plasma membrane. Furthermore, analysis of apoptotic markers confirmed that infected A549 cells underwent apoptosis at later stages. In addition, inhibition of internalization of NTHi by cytochalasin D prevented apoptosis of cells. Collectively, these findings suggest that internalization of NTHi and its escape from vacuolar compartments triggers cytotoxicity of alveolar cells via apoptosis during the infection process.This article is protected by copyright. All rights reserved.
    Pathogens and Disease. 09/2014;
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    ABSTRACT: Background. There is evidence that Tregs are important to prevent allergic diseases like asthma but limited literature exists on role of TH17 cells in allergic diseases. Methods. Fifty children with asthma and respiratory allergy (study group) and twenty healthy children (control group) were recruited in this study. Total IgE levels and pulmonary function tests were assessed. The expression of Tregs and cytokines was determined by flow cytometry. Results. The average level of total IgE in study group (316.8 ± 189.8 IU/mL) was significantly higher than controls (50 ± 17.5 IU/mL, P < 0.0001). The frequency of TH17 cells and culture supernatant level of IL-17 in study group (12.09 ± 8.67 pg/mL) was significantly higher than control group (2.01 ± 1.27 pg/mL, P < 0.001). Alternatively, the frequency of FOXP3 level was significantly lower in study group [(49.00 ± 13.47)%] than in control group [(95.91 ± 2.63)%] and CD4(+)CD25(+)FOXP3(+) to CD4(+)CD25(+) ratio was also significantly decreased in study group [(6.33 ± 2.18)%] compared to control group [(38.61 ± 11.04)%]. The total serum IgE level is negatively correlated with FOXP3 level (r = -0.5273, P < 0.0001). The FOXP3 expression is negatively correlated with the IL-17 levels (r = -0.5631, P < 0.0001) and IL-4 levels (r = -0.2836, P = 0.0460). Conclusions. Imbalance in TH17/Tregs, elevated IL-17, and IL-4 response and downregulation of FOXP3 were associated with allergic asthma.
    International Journal of Pediatrics 06/2014;
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    ABSTRACT: Hepatitis B virus (HBV) cccDNA levels is an absolute marker of HBV replication in the liver of HBV infected patients. This study aimed to quantify the HBV cccDNA levels in sera and liver tissue samples of treatment naïve patients with chronic hepatitis B. Eighty one chronic hepatitis B (CHB) treatment naïve patients were enrolled from January 2009 to June 2011. Total HBV DNA and HBV cccDNA levels were quantified using sensitive real time PCR assay. The mean age of recruited patients was 34 ± 11.5 years. Fifty four (66.7 %) patients were HBeAg negative. Liver tissue samples were available from 2 HBeAg positive and 21 HBeAg negative CHB patients. The amount of total intrahepatic HBV DNA ranged from 0.09 to 1508.92 copies/cell. The median intrahepatic HBV cccDNA was 0.31 and 0.20 copies/cell in HBeAg positive and HBeAg negative cases, respectively. Serum HBV cccDNA was detectable in 85.2 % HBeAg positive and 48.1 % HBeAg negative CHB patients. Median serum HBV cccDNA was 46,000 and 26,350 copies/mL in HBeAg positive and HBeAg negative subjects, respectively. There was a significant positive correlation between the levels of intrahepatic total HBV DNA and intrahepatic HBV cccDNA (r = 0.533, p = 0.009). A positive correlation was also seen between serum HBV cccDNA levels and serum HBV DNA levels (r = 0.871, p < 0.001). It was concluded that serum HBV cccDNA could be detectable in higher proportion of HBeAg positive patients compared to HBeAg negative patients. Moreover, the median level of serum HBV cccDNA was significantly higher in HBeAg positive patients in contrast to HBeAg negative subjects.
    Molecular Biology Reports 04/2014; · 2.51 Impact Factor
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    ABSTRACT: Introduction. Hepatitis C virus (genotype-3) causes acute and chronic hepatitis infection predomination in India. The infectious phase of the virus requires various host factors for its survival and subsequent viral particle production. Small RNA molecules like microRNA-122 (miR-122) are one such factor mostly present in the liver and play a supportive role in viral replication. Objective. In this study, diagnostic potential of miR-122 is evaluated in the sera of chronic hepatitis C patients. Methods. miRNAs were isolated from the sera samples of patients as well as controls and miR-122 expression was quantified by real-time PCR. Results. A significant augmentation was observed in the level of circulating miR-122 (median level, 0.66 versus 0.29, P = 0.001) in patients compared to controls with ROC value of 0.929 ± 0.034 (P < 0.001). Interestingly, miR-122 level also depicted a significant positive correlation with serum ALT (r = 0.53), AST (r = 0.44), and viral load (r = 0.52). Conclusion. The study thus unveiled the role of miR-122 as a plausible diagnostic biomarker during HCV genotype-3 infection in India.
    Disease markers 01/2014; 2014:435476. · 2.14 Impact Factor
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    ABSTRACT: Group A streptococcus (GAS, Streptococcus pyogenes) type emm1 is widely associated with streptococcal invasive disease. This type is prevalent worldwide but is rare in India. Instead, emm1-2 type which is closely related to emm1 but is a distinct type is more prevalent. Although emm1 has been well characterized, information available on emm1-2 is rare. In this study we present a comparative study of both types. DNA microarray analysis showed segregation of emm1 and emm1-2 isolates into two distinct clusters. Out of 229 arrayed genes, 83-87% were present, 6-9% absent and 4-8% genes were ambiguous in emm1 isolates. emm1-2 strains harbored only 68-77%, 11-13% were absent and 10-20% ambiguous genes. Fourteen genes, present in all emm1, were completely absent in the emm1-2 isolates. sfb1 is a gene which encodes for Streptococcal fibronectin binding adhesin and invasin which has restricted distribution among different emm types of GAS. A variant of sfb1 (sfb1-2) was the only gene which was present in all emm1-2 isolates, but absent from all emm1 strains. Sfb1 and Sfb1-2 differ in sequences in the aromatic domain and the proline rich repeat region, whereas the fibronectin binding region was conserved and exhibited similar fibronectin binding activity. The presence of Sfb1-2 in emm1-2 strains was concomitant with significantly higher fibronectin-binding and invasion efficiency of HEp-2 cells when compared to emm1 isolates. The role of Sfb1-2 in invasion was confirmed by latex bead assay. emm1-2 isolates follow membrane ruffling mechanism during invasion and intracellularly follow classical endocytic pathway. Further studies are required to understand the correlation between the presence of emm1-2 isolates and the disease pattern in North India.
    International Journal of Medical Microbiology. 01/2014;
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    ABSTRACT: In vitro and in vivo studies have suggested that reduced astrocytic uptake of neuronally released glutamate, alterations in expression of glial fibrillary acidic protein (GFAP) and aquaporin-4 (AQP-4) contribute to brain edema in acute liver failure (ALF). However, there is no evidence to date to suggest that these alterations occur in patients with ALF. We analyzed the mRNA expression of excitatory amino acid transporters (EAAT-1, EAAT-2), GFAP and AQP-4 in the cerebral cortex obtained at autopsy from 8 patients with ALF and from 7 patients with no evidence of hepatic or neurological disorders by real-time PCR, and protein expression was assessed using immunoblotting and immunohistochemistry. We demonstrated a significant decrease in GFAP mRNA and protein levels in ALF patients compared to controls. While the loss of EAAT-2 protein in ALF samples was post-translational in nature, EAAT-1 protein remained within normal limits. Immunohistochemistry confirmed that, in all cases, the losses of EAAT-2 and GFAP were uniquely astrocytic in their localization. AQP-4 mRNA expression was significantly increased and its immunohistochemistry demonstrated increased AQP-4 immunoreactivity in the glial end-feet process surrounding the microvessels. These findings provide evidence of selective alterations in the expression of genes coding for key astrocytic proteins implicated in central nervous system (CNS) excitability and brain edema in human ALF. This article is protected by copyright. All rights reserved.
    Journal of Neurochemistry 10/2013; · 3.97 Impact Factor
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    ABSTRACT: Tumor angiogenesis, a major requirement for tumor growth and metastasis, is regulated by pro- and anti-angiogenic factors. The aim of this study was to quantify the expression of angiogenic (VEGF, HIF-1α, Angiopiotein-2) and anti-angiogenic (endostatin, angiostatin and Thrombospondin-1) factors and to discern their clinical relevance. A total 90 patients (67 HCC, 9 cirrhosis and 14 chronic hepatitis) were enrolled in the study. Tissue transcript levels of angiogenic (VEGF, HIF-1α, Ang-2) and anti-angiogenic (endostatin, angiostatin and TSP-1) factors were analyzed by quantitative real time-polymerase chain reaction (qRT-PCR) in the tissue samples. The tissue transcript levels of VEGF, HIF-1α and endostatin were found to be significantly higher in HCC in comparison to cirrhosis and chronic hepatitis. Although Ang-2, angiostatin and TSP-1 tissue transcript levels were higher in HCC group than the others groups but the difference was not statistically significant. In univariate analysis both VEGF and HIF-1α were found to be associated with poor survival of HCC patients. Multivariate analysis by the cox proportional hazard model revealed only VEGF as an independent factor predicting poor survival of the HCC patients. Angiogenic and anti-angiogenic factors are all highly expressed in HCC patients. Upregulation of tissue anti-angiogenic factors indicates the urgency for the alternative of anti-angiogenic therapies.
    Molecular Biology Reports 09/2013; · 2.51 Impact Factor
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    Journal of Viral Hepatitis 09/2013; 20(s3). · 3.08 Impact Factor
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    ABSTRACT: Hepatocellular carcinoma (HCC) is a prototype tumor wherein angiogenesis plays a vital role in its progression. The role of VEGF, a major angiogenic factor in HCC is known; however, the role of anti-angiogenic factors simultaneously with the angiogenic factors has not been studied before. Hence, in this study, the serum levels of major angiogenic [Vascular Endothelial Growth Factor (VEGF), angiopoietin-2 (Ang-2)] and anti-angiogenic (endostatin, angiostatin) factors were analyzed and correlated with clinico-radiological features and with outcome. A total of 150 patients (50 HCC, 50 cirrhosis and 50 chronic hepatitis) and 50 healthy controls were enrolled in this study. Serum levels of VEGF, Ang-2, endostatin, and angiostatin were estimated by enzyme-linked immunosorbent assay. HCC shows significantly elevated serum levels of angiogenic factors VEGF and Ang-2 and of anti-angiogenic factors endostatin and angiostatin. ROC curve analysis for serum VEGF yielded an optimal cut-off value of 225.14 pg/ml, with a sensitivity of 78 % and specificity of 84.7 % for a diagnosis of HCC and its distinction from other group. Using this value, the univariate and multivariate analysis revealed significantly poor outcome in patients with higher levels of serum VEGF (p = 0.009). Combinatorial analysis revealed that patients with higher levels of both angiogenic and anti-angiogenic factors showed poor outcome. Serum VEGF correlates with poor survival of HCC patients and, therefore, serves as a non-invasive biomarker of poor prognosis. Moreover, elevated levels of anti-angiogenic factors occur endogenously in HCC patients.
    Molecular and Cellular Biochemistry 08/2013; · 2.33 Impact Factor
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    ABSTRACT: Mutations in the reverse transcriptase (RT) region of the hepatitis B virus (HBV) genome lead to decreased susceptibility to nucleos(t)ide analogs approved for treatment of HBV infection. The aim of this study was to detect and analyze pre-existing HBV RT mutations in treatment naïve patients with chronic hepatitis B. Seventy one chronic HBV treatment naïve patients were enrolled from January 2009 to June 2011. HBV RT sequence analysis was done by using direct bidirectional sequencing of semi-nested PCR products. HBV genotypes were determined by multiplex PCR. Genotype D was found in 64 patients (90.1%) followed by genotype C and A which were present in 5 (7.0%) and 2 (2.8%) patients respectively. The results of the RT sequence analysis showed mutations in 34 (47.9%) patients. The rtH248N mutation was the most common mutation, accounting for 47.1% patients. Other common mutations included rtD263E/S, rtM129L, rtF122L/V/I, rtS135Y/H, rtQ149K, rtL91I, rtH126R, rtC256S/G, rtY257W, rtS259T and rtE271D, which were present in 26.5% (9/34), 29.4% (10/34), 20.6% (7/34), 20.6% (7/34), 20.6% (7/34), 17.6% (6/34), 14.7% (5/34), 14.7% (5/34), 11.8% (4/34), 11.8% (4/34) and 11.8% (4/34) patients respectively. The known primary drug resistance mutations were found in 3 (8.8%) patients. The present study shows the presence of RT amino acid substitutions in treatment-naïve patients with chronic hepatitis B, which may decrease susceptibility to available oral antiviral drugs. On the basis of the finding of this study, genotypic testing is recommended before the start of therapy in naïve patients, so that suitable antiviral drugs can be prescribed. J. Med. Virol. 85:1155-1162, 2013. © 2013 Wiley Periodicals, Inc.
    Journal of Medical Virology 07/2013; 85(7):1155-62. · 2.37 Impact Factor
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    ABSTRACT: MicroRNAs (miRNAs) are a versatile class of tiny non-coding RNAs involved in regulation of various biological processes. miRNA-122 (miR-122) is specifically and abundantly expressed in human liver. However, the role of miR-122 in differentiation of fetal liver stem/progenitor cells into hepatocytes remains unclear. In this study, dual positive CD34+/CD117+ expressing human fetal liver stem/progenitor cells was enriched by magnetic cell sorting and cultured in vitro. The level of miR-122 was found to be increased at specific time intervals. Interestingly, during the differentiation process of hepatocyte-like cells, the increase in expression of miR-122 was positively correlated with expression of hepatocyte-specific genes. The status of differentiation process was improved by transfection of miR-122 into enriched stem/progenitor cells. The expression level of hepatic-specific genes as well as liver-enriched transcription factors (LETFs) was significantly increased by overexpression of miR-122 in fetal liver stem/progenitor cells. Thus, the study delineated the role of hepato-specific miR-122 in differentiation of fetal liver stem/progenitor cells into hepatocyte-like cells which could be used as a therapeutic target molecule to generate abundant hepatocytes. J. Cell. Biochem. © 2013 Wiley Periodicals, Inc.
    Journal of Cellular Biochemistry 01/2013; · 3.06 Impact Factor
  • The Indian Journal of Medical Research 01/2012; 135:133-6. · 2.06 Impact Factor
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    ABSTRACT: Viral hepatitis is a major cause of mortality and morbidity in developing countries. Hepatitis E virus (HEV) is responsible for both sporadic and epidemic outbreaks of viral hepatitis in India. Here a total of 843 samples were collected: 685 from patients with acute viral hepatitis (AVH), 70 from patients with fulminant hepatic failure (FHF), 53 from patients with chronic liver disease (CLD), 11 from patients with antituberculosis therapy (ATT)-induced jaundice, and 24 from pregnant women. When tested for anti-HEV IgM, 58.3% of the pregnant women, 41.4% of the patients with FHF, 38.6% of the patients with AVH, 9.4% of the patients with CLD, and 18.2% of the patients with ATT-induced jaundice tested positive. We found that 34% and 16% of the acute hepatitis patients and fulminant hepatitis patients, respectively, showed no reactivity to the existing viral hepatitis markers and were thus grouped as non A to E. Among the HEV IgM-positive cases, males outnumbered females (62.8% versus 37.1%). HEV RNA was found in 35% of fulminant and 9.4% of acute hepatitis patients. From phylogenetic analysis, we observed that all the isolates were clustered within genotype 1. Critical analysis placed the acute isolates along with strains under subtype Ia, while the fulminant isolates clustered along with the FHF strain (X98292) under subtype Ic. The segregation of HEV isolates from AVH and FHF patients into different subtypes raises interesting questions on the molecular basis of HEV disease severity.
    Diagnostic microbiology and infectious disease 08/2011; 71(2):110-7. · 2.45 Impact Factor
  • V Dhanda, R Kumar, J S Thakur, A Chakraborti
    The Indian Journal of Medical Research 12/2010; 132:741-4. · 2.06 Impact Factor
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    ABSTRACT: Hepatitis E is endemic to the Indian subcontinent, with a seroprevalence of 4-20%, and more than 25% of acute viral hepatitis is due to HEV. The northern parts of India have been experiencing outbreaks and sporadic cases of HEV since 1955. In a total of sixteen HEV sequences, ten acute viral hepatitis and 6 fulminant hepatic failure cases were analysed. Subtypes 1a and 1c of HEV are prevalent in North India, with the subtype-1c showing a trend towards fulminancy.
    Archives of Virology 09/2010; 155(9):1483-6. · 2.28 Impact Factor
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    Pujhari SK, Kumar S, Ratho RK, Chawla YK, Chakraborti A
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    ABSTRACT: Hepatitis E is endemic to the Indian subcontinent, with a seroprevalence of 4-20%, and more than 25% of acute viral hepatitis is due to HEV. The northern parts of India have been experiencing outbreaks and sporadic cases of HEV since 1955. In a total of sixteen HEV sequences, ten acute viral hepatitis and 6 fulminant hepatic failure cases were analysed. Subtypes 1a and 1c of HEV are prevalent in North India, with the subtype-1c showing a trend towards fulminancy.
    Arch Virol. 08/2010; 155(9):1483-6.
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    ABSTRACT: Data on genotypes, basal core promoter (BCP) and precore mutants of hepatitis B virus and their association with different HBV related liver disease have been studied inadequately and are controversial. Thus, the aim of this study was to determine the incidence of BCP and precore HBV mutants and their relationship with HBV genotype and different stages of HBV related liver disease in North Indian patients. A total 273 patients with different stages of HBV related liver diseases were enrolled. Nested polymerase chain reaction (PCR) was used to amplify the BCP/PC regions. RFLP and direct sequencing were performed to validate the mutations identified in these regions. HBV genotyping was accomplished by multiplex PCR. Genotype D was the predominant genotype found in each of the various HBV related liver diseases. The BCP mutation was found significantly more often in inactive carriers and compensated cirrhosis as compared to the other groups. The BCP mutation was present in 29.1% of patients with genotype D versus 17.1% with genotype A (P = 0.001). The precore mutation was also more frequently observed with genotype D compared with genotype A (36.9 vs. 4.8%, P = 0.0007). Genotype D is predominant in North Indian patients. The BCP and precore mutations occur in one-third of HBV positive patients in association with the genotype D. We did not find any correlation with severity of liver disease with genotypes and mutations.
    Digestive Diseases and Sciences 03/2010; 55(3):794-802. · 2.26 Impact Factor
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    P Kaur, A Chakraborti, A Asea
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    ABSTRACT: Enteroaggregative Escherichia coli (EAEC) are quite heterogeneous category of an emerging enteric pathogen associated with cases of acute or persistent diarrhea worldwide in children and adults, and over the past decade has received increasing attention as a cause of watery diarrhea, which is often persistent. EAEC infection is an important cause of diarrhea in outbreak and non-outbreak settings in developing and developed countries. Recently, EAEC has been implicated in the development of irritable bowel syndrome, but this remains to be confirmed. EAEC is defined as a diarrheal pathogen based on its characteristic aggregative adherence (AA) to HEp-2 cells in culture and its biofilm formation on the intestinal mucosa with a "stacked-brick" adherence phenotype, which is related to the presence of a 60 MDa plasmid (pAA). At the molecular level, strains demonstrating the aggregative phenotype are quite heterogeneous; several virulence factors are detected by polymerase chain reaction; however, none exhibited 100% specificity. Although several studies have identified specific virulence factor(s) unique to EAEC, the mechanism by which EAEC exerts its pathogenesis is, thus, far unknown. The present review updates the current knowledge on the epidemiology, chronic complications, detection, virulence factors, and treatment of EAEC, an emerging enteric food borne pathogen.
    Interdisciplinary Perspectives on Infectious Diseases 01/2010; 2010:254159.
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    ABSTRACT: The outcome of hepatitis C virus (HCV) infection is determined by the interplay between the virus and the host immune response. Interleukin (IL)-18, an interferon-gamma-inducing factor, plays a critical role in the T helper type 1 (Th1) response required for host defence against viruses, and antibodies to IL-18 have been found to prevent liver damage in a murine model. The present study was conducted to investigate the possible role of IL-18 in the pathogenesis and persistence of HCV. IL-18 levels were measured in sera of 50 patients at various stages of HCV infection (resolved, chronic and cirrhosis) and compared with those of normal controls. IL-18 gene expression was studied in peripheral blood mononuclear cells (PBMC) from each group, and in liver biopsy tissue from patients with chronic hepatitis C. The mean levels of IL-18 in sera were markedly elevated in patients with chronic hepatitis and cirrhosis, and were reduced in patients with resolved HCV infection. The serum IL-18 concentrations were related to the Child-Pugh severity of liver disease in cirrhotic patients. There also existed a strong positive correlation of IL-18 levels with histological activity score and necrosis. IL-18 mRNA expression was significantly up-regulated in the PBMC of cirrhotic patients when compared with other groups, while in the liver, higher levels of IL-18 transcripts were expressed in patients with chronic hepatitis C. The results of our study indicate that IL-18 levels reflect the severity and activity of HCV infection, and may contribute to the pathogenesis and progression of liver disease associated with HCV.
    Immunology 09/2009; 128(1 Suppl):e514-22. · 3.71 Impact Factor
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    ABSTRACT: Telomerase expression and the maintenance of a critical telomere length (TL) in cancer initiation indicates that telomere shortening and telomerase expression initiates cancer by induction of chromosomal instability. Telomerase activity, TL and human telomerase reverse transcriptase (hTERT) expression were investigated in 58 hepatocellular carcinoma (HCC) and 17 chronic hepatitis patients by the telomerase repeat amplification protocol, Southern blotting and reverse transcriptase-polymerase chain reaction. Telomerase was positive in 76% of HCC and 11.8% of chronic hepatitis patients (P<0.0001). The mean telomere length (MTL) in HCC was significantly shorter compared with chronic hepatitis (P<0.0001). The MTL was not significantly different in HCC patients with and without cirrhosis (P=0.77). In hepatitis B virus, hepatitis C virus and non-B non-C-related HCC groups, no differences were found in telomerase activity and MTL (P=0.77). hTERT, a regulator of telomerase, was, however, positive in 81% of HCCs. The correlation between telomerase activity and hTERT mRNA expression was statistically significant (P<0.0001). The MTL in telomerase-positive HCC cases was significantly shorter than the MTL in telomerase-negative cases (P<0.0001). The majority of HCCs exhibited telomerase activity that correlated well with hTERT expression. MTL in HCC was significantly shorter than chronic hepatitis. It was also found that shorter telomeres are present in telomerase-positive HCC cases. However, no correlation was found between telomerase activity and TL with respect to the viral status in HCC.
    Liver international: official journal of the International Association for the Study of the Liver 08/2009; 29(8):1162-70. · 3.87 Impact Factor