Biomedical subjects

Soma Das

Publications and source records attributed to Soma Das.

44 records · Page 3Linked to original sources

PubMed2003

Interethnic difference in the allelic distribution of human epidermal growth factor receptor intron 1 polymorphism.

PURPOSE: Epidermal growth factor receptor (EGFR) plays a critical role in signal transduction and is a target for a novel class of anticancer agents that aim to inhibit EGFR-mediated cancer cell growth. Previous studies have demonstrated a dinucleotide (CA)(n) repeat polymorphism in intron 1 of EGFR, ranging from 14 to 21 repeats, that has been suggested to regulate EGFR expression. The longer allele with 21 repeats showed an 80% reduction of gene expression compared with the shorter allele with 16 repeats. Therefore, the evaluation of the allelic distribution of this polymorphism in populations of various ethnic origins will be crucial to understand the interindividual variability in EGFR expression. EXPERIMENTAL DESIGN: We evaluated the influence of ethnicity on this polymorphism by genotyping individuals of Caucasian (n = 183), African-American (n = 84), and Asian (n = 66) background. RESULTS: The frequency of one of the longer alleles, allele 20 is significantly higher in Asian individuals (63% compared with 21% in Caucasians, P = 2 x 10(-18)). In confirmation of prior studies, the shorter allele 16 was the most common allele in Caucasians (43%) and African-Americans (42%), but its frequency was significantly lower in Asians (average 17%, P = 10(-7) compared with Caucasians). CONCLUSION: Major interethnic differences in the allelic frequencies of the EGFR intron 1 polymorphism exist. Our results may contribute to a better understanding of the molecular basis underlying ethnic differences in drug response and may be helpful for future strategies of individualized therapy with EGFR inhibitors.

Alleles↗

PubMed2002

Loss of PTEN expression is associated with metastatic disease in patients with endometrial carcinoma.

BACKGROUND: The PTEN tumor suppressor gene frequently is involved in endometrial carcinoma. Loss of heterozygosity and mutations reportedly are common, although the biologic importance of these changes remain largely unknown. The objective of this study was to assess the pattern of PTEN expression by immunohistochemistry in a large series of patients with endometrial carcinoma. METHODS: A population-based series of 316 patients with endometrial carcinoma who had long and complete follow-up was investigated for PTEN expression and its correlation with clinicopathologic variables, tumor markers, and survival. RESULTS: PTEN protein expression was mainly cytoplasmic in tumor cells, with no expression seen in 56 of 279 patients (20%) who had evaluable results. A heterogeneous staining pattern was found in 70 tumors (25%). A significant association between the loss of PTEN expression and metastatic disease was identified (P = 0.05). However, PTEN staining did not influence survival significantly. CONCLUSIONS: The loss of PTEN expression is relatively frequent in endometrial carcinoma and is associated significantly with metastatic disease. This indicates that the PTEN system plays an important role in some endometrial carcinomas, but further studies of PTEN protein expression related to various genetic alterations are necessary.

Adenocarcinoma, Clear Cell↗

PubMed2002

Clinical and molecular basis of classical lissencephaly: Mutations in the LIS1 gene (PAFAH1B1).

Classical lissencephaly (LIS) and subcortical band heterotopia (SBH) are related cortical malformations secondary to abnormal migration of neurons during early brain development. Approximately 60% of patients with classical LIS, and one patient with atypical SBH have been found to have deletions or mutations of the LIS1 gene, located on 17p13.3. This gene encodes the LIS1 or PAFAH1B1 protein with a coiled-coil domain at the N-terminus and seven WD40 repeats at the C-terminus. It is highly conserved between species and has been shown to interact with multiple proteins involved with cytoskeletal dynamics, playing a role in both cellular division and motility, as well as the regulation of brain levels of platelet activating factor. Here we report 65 large deletions of the LIS1 gene detected by FISH and 41 intragenic mutations, including four not previously reported, the majority of which have been found as a consequence of the investigation of 220 children with LIS or SBH by our group. All intragenic mutations are de novo, and there have been no familial recurrences. Eight-eight percent (36/41) of the mutations result in a truncated or internally deleted protein-with missense mutations found in only 12% (5/41) thus far. Mutations occurred throughout the gene except for exon 7, with clustering of three of the five missense mutations in exon 6. Only five intragenic mutations were recurrent. In general, the most severe LIS phenotype was seen in patients with large deletions of 17p13.3, with milder phenotypes seen with intragenic mutations. Of these, the mildest phenotypes were seen in patients with missense mutations.

1-Alkyl-2-acetylglycerophosphocholine Esterase↗

PubMed2002

Characterization of mutations in fifty North American patients with X-linked myotubular myopathy.

X-linked myotubular myopathy (MTM1) is a rare developmental disorder of skeletal muscle that is characterized by the presence of abnormal central nuclei in biopsy specimens taken from affected individuals. To date 133 different mutations have been identified in the MTM1 gene worldwide. We report here mutations detected in 50 additional U.S. families with biopsy-proven MTM1. Forty-one of the patients have not been described previously, including 18 with novel mutations. Eighty-eight percent of the mothers of sporadic cases that were studied were identified as carriers, extending the previously reported high-carrier frequency for this disorder. Clinical information collected on the majority of patients helps to further correlate genotype with phenotype, and implications of these data for genetic counseling in families are discussed.

Adolescent↗

PubMed2002

Subcortical band heterotopia (SBH) in males: clinical, imaging and genetic findings in comparison with females.

Subcortical band heterotopia (SBH) or double cortex syndrome is a neuronal migration disorder, which occurs very rarely in males: to date, at least 110 females but only 11 in males have been reported. The syndrome is usually associated with mutations in the doublecortin (DCX) (Xq22.3-q23) gene, and much less frequently in the LIS1 (17p13.3) gene. To determine whether the phenotypic spectrum, the genetic basis and genotype-phenotype correlations of SBH in males are similar to those in females, we compared the clinical, imaging and molecular features in 30 personally evaluated males and 60 previously reported females with SBH. Based on the MRI findings, we defined the following band subtypes: partial, involving one or two cerebral lobes; intermediate, involving two lobes and a portion of a third; diffuse, with substantial involvement of three or more lobes; and pachygyria-SBH, in which posterior SBH merges with anterior pachygyria. Karyo typing and mutation analysis of DCX and/or LIS1 were performed in 23 and 24 patients, respectively. The range of clinical phenotypes in males with SBH greatly overlapped that in females. MRI studies revealed that some anatomical subtypes of SBH, such as partial and intermediate posterior, pachygyria-SBH and diffuse bands with posterior predominance, were more frequently or exclusively present in males. Conversely, classical diffuse SBH and diffuse bands with anterior predominance were more frequent in females. Males had either mild or the most severe band subtypes, and these correlated with the over-representation of normal/borderline intelligence and severe mental retardation, respectively. Conversely, females who had predominantly diffuse bands exhibited mostly mild or moderate mental retardation. Seven patients (29%) had missense mutations in DCX; in four, these were germline mutations, whereas in three there was evidence for somatic mosaicism. A germline missense mutation of LIS1 and a partial trisomy of chromosome 9p were identified in one patient (4%) each. One male each had a possible pathogenic intronic base change in both DCX and LIS1 genes. Our study shows that SBH in males is a clinically heterogeneous syndrome, mostly occurring sporadically. The clinical spectrum is similar to that of females with SBH. However, the greater cognitive and neuroradiological heterogeneity and the small number of mutations identified to date in the coding sequences of the DCX and LIS1 genes in males differ from the findings in females. This suggests other genetic mechanisms such as mutations in the non-coding regions of the DCX or LIS1 genes, gonadal or somatic mosaicism, and finally mutations of other genes.

1-Alkyl-2-acetylglycerophosphocholine Esterase↗

PubMed2002

Haplotype structure of the UDP-glucuronosyltransferase 1A1 promoter in different ethnic groups.

Genetic variation in UDP-glucuronosyltransferase 1A1 (UGT1A1)expression has several important clinical implications. UGT1A1 basal transcription is affected by a polymorphic (TA)n repeat, and another important regulatory element is the phenobarbital-responsive enhancer module (PBREM) which might contain variants affecting inducible gene expression. We assessed the extent of linkage disequilibrium between the (TA)n polymorphism and variants in the PBREM and UGT1A1 promoter. We also investigated the relationship between PBREM-(TA)n haplotypes and the glucuronidation rate of the UGT1A1 substrate SN-38. DNAs from 83 human livers were genotyped for the (TA)n polymorphism and microsomes from the same livers were phenotyped for SN-38 glucuronidation. The (TA)n polymorphism was genotyped in 24 additional African-Americans included in the Human Variation Panel (Coriell Institute). A 606-bp region spanning the PBREM was sequenced in 81 liver and a subset of 22 Human Variation Panel DNAs and six variants were found. The -3279G T and -3156G A variants are common (0.39 and 0.30, respectively). -3279G T is more common in Caucasians than African-Americans (P = 0.001). In Caucasians, linkage disequilibrium was highly significant between sites -3279, -3156, and the (TA)n polymorphism (P < 0.0001). In contrast, in African-Americans, only marginal levels of significance were observed between (TA)n and -3279 (P = 0.02) and between -3279 and -3156 (P = 0.04). Ten promoter haplotypes were identified. Haplotype I is the most common (0.39), from which haplotype II (0.15) differs at position -3279. SN-38G formation rates were correlated with (TA)n genotypes. This study showed that (i) common promoter variants are in linkage disequilibrium and (ii) the haplotype structure of promoter is probably different between Caucasians and African-Americans.

Black or African American↗

PubMed2002

Genomic diversity of group A rotavirus strains infecting humans in eastern India.

Between 1998 and 2000, a total of 266 samples were found positive for group A rotaviruses by RNA electrophoresis. Samples were collected from patients admitted to two leading hospitals in Calcutta. Serotyping could be done only with 22% of the positive samples, leaving 78% untypeable. The G (VP7 genotypes) and P (VP4 genotypes) types were determined for 159 samples by reverse transcription and multiplex PCR. The predominant genotype was G1P[8] (20%), followed by G2P[4] (15%) and G4P[8] (6%). A number of uncommon genotypes, G1P[4] (4%), G2P[8] (2.5%), G2P[6] (0.6%), G4P[4] (2.5%), and G4P[6] (1.25%), were also detected during this study period. Twenty two percent of specimens showed mixed infections, 38 (24%) of the total samples remained untypeable for either VP7 or VP4, while only 4 (2.5%) of the samples were untypeable for both genes. Eleven specimens collected from Manipur were also genotyped and revealed a very high degree of genomic reassortment.

Child, Preschool↗

PubMed2002

Loss of hMSH2 and hMSH6 expression is frequent in sporadic endometrial carcinomas with microsatellite instability: a population-based study.

Microsatellite instability (MSI) seems to be important in the development of various human cancers including sporadic endometrial cancer. It has previously been shown that alterations in the mismatch repair gene hMLH1 seem to be important for the development of MSI in these tumors. The role of the other mismatch repair genes hMSH2 and hMSH6 has been less well studied, but investigations on patients with hereditary nonpolyposis colorectal cancer indicate that these genes also may be involved. We therefore wanted to investigate the pattern of hMSH2 and hMSH6 expression in a prospective and population-based series of endometrial carcinomas with known hMLH1 expression and MSI status. A total of 138 patients were studied, and pathological staining was seen in 19 cases (14%) for hMLH1, 26 cases (19%) for hMSH2, and 17 cases (12.3%) for hMSH6. Pathological hMLH1 expression was more frequent among tumors with high MSI (those positive for four to five of five markers), whereas pathological expression of hMSH2 and hMSH6 was more frequent among tumors with intermediate MSI (those positive for two to three of five markers). MSI was significantly correlated with pathological expression of hMLH1 (P < 0.001), hMSH2 (P = 0.04), and hMSH6 (P = 0.001). In the group with high MSI, 14 of 16 tumors (88%) showed pathological expression for at least one of the markers. The expression of hMLH1, hMSH2, or hMSH6 did not significantly influence survival. In conclusion, pathological expression of hMLH1 does not seem to account for all tumors with a MSI-positive phenotype in this population-based series of endometrial carcinomas. Our data indicate that the other mismatch repair genes hMSH2 and hMSH6 are also involved, especially in cases with intermediate MSI.

Adaptor Proteins, Signal Transducing↗