Anu Ghosh

Indian ethnic populations characterized by dopamine (D4) receptor VNTR polymorphism.

Background: The human dopamine receptor D4 gene (DRD4) contains a 48-bp tandem repeat in exon 3 and shows alleles varying between repeats 2 and 11. The gene shows a high level of expression in the prefrontal cortex of the brain and association of particular alleles of this locus with various neuropsychiatric and personality disorders have been reported. Objective: The present study reports allele frequency distribution at the DRD4 variable number tandem repeat (VNTR) locus among five ethnic populations of India. This background information is fundamental to the field of pharmacogenetics for disease susceptibility and association studies. Subjects and methods: Three hundred and thirty two healthy unrelated adult individuals belonging to five ethnic groups: Konkanastha Brahmins, Marathas, Ezhavas, Nairs and Muslims, have been typed. Genomic DNA, extracted from peripheral blood, was PCR amplified using a two-enzyme system. The use of ALF™Express DNA sequencer was found to be helpful for large-scale population genotyping. Statistical analysis was performed using the POPGENE and DISPAN programs. Results: A total of eight alleles ranging from repeat 2 to repeat 9 were observed. Allele 4 was the predominant allele among all the five populations, consistent with the data on other world populations. A rare allele 9 was detected exclusively among Marathas. The observed heterozygosity was low, ranging from 0.38 to 0.54 while other parameters like Polymorphism Information Content (PIC) and Power of Discrimination (PD) showed moderate values. The populations were in genetic equilibrium when tested under Hardy–Weinberg expectations. Conclusion: The allele frequency estimates for DRD4 provided here will contribute towards developing an informative database for this functionally relevant locus. This will prove useful when studying the association between genetic factors and pathogenesis of disease in Indian populations and will address the concern of biased results of association due to population admixtures. Résumé. Le gène D4 récepteur de la dopamine humaine (DRD4) contient un tandem répété de 48-bp en exon 3 et présente des allèles variant entre les répétitions 2 et 11. Le gène présente un niveau élevé d’expression dans le cortex frontal du cerveau et on a fait état de diverses affections neuropsychiatriques et de troubles de personnalité en association avec les gènes de ce locus. Objectif: Cette étude concerne la distribution de fréquence allélique du nombre variable de répétitions de tandem (VNTR) au locus DRD4 dans cinq populations ethniques de l’Inde. Cette information d’arrière plan est fondamentale pour les études de susceptibilité et d’associations pathologiques en pharmacogénétique. Sujets et méthodes: On a typé 332 adultes sains et non apparentés, appartenant à cinq groupes ethniques : Konkanastha Brahmin, Maratha, Ezhava, Nair et des musulmans. L’ADN génomique extrait du sang périphérique, a été amplifié par PCR au moyen d’un système de deux enzymes. L’utilisation du séquenceur d’ADN ALFTM a été efficace pour le génotypage à grande échelle. Les analyses statistiques ont été effectuées à l’aide des programmes POPGENE et DISPAN. Résultats: On a observé au total huit allèles, variant de la répétition 2 à la répétition 9, l’allèle 4 étant prédominant dans les cinq populations, en accord avec les données mondiales. Un rare allèle 9 a été trouvé chez Maratha exclusivement. L’hétérozygosité observée est faible, variant de 0,38 à 0,54, tandis que d’autres paramètres tels le Contenu d’Information Polymorphique et le Pouvoir de Discrimination présentent des valeurs modérées. Les populations testées par rapport aux proportions de Hardy-Weinberg apparaissent en équilibre génétique. Conclusion: Ces estimations de fréquences alléliques pour DRD4 contribueront au développement d’une base de données sur ce locus. Ceci sera utile pour l’étude de l’association entre facteurs génétiques et pathogenèse dans les populations indiennes et nourrira le problème des biais de résultats d’association dus aux mélanges de populations. Zusammenfassung.Hintergrund: Das menschliche Dopaminrezeptor-D4-Gen (DRD4) enthält ein 48-bp-Tandem-Repeat in Exon 3 und zeigt Allele, die zwischen den Repeats 2 und 11 variieren. Das Gen zeigt eine starke Ausprägung im präfrontalen Cortex des Gehirns, und es wurden Beziehungen zwischen besonderen Allelen dieses locus und verschiedenen neuropsychiatrischen und Persönlichkeitsstörungen berichtet. Vorhaben: Die vorliegende Untersuchung berichtet über die Verteilung der Allelhäufigkeiten am DRD4-VNTR-locus (variable number tandem repeat, VNTR, verschiedene Anzahl von Tandem-Repeats) bei fünf ethnischen Bevölkerungsgruppen in Indien. Diese Hintergrundinformation ist wesentlich auf dem Gebiet der Pharmakogenetik für Krankheitsanfälligkeit und Assoziationsstudien. Probanden und Methoden: 332 gesunde, nicht verwandte Personen aus fünf ethnischen Gruppen, Konkanastha Brahmins, Marathas, Ezhavas, Nairs und Moslems, wurden typisiert. Genomische DNS aus peripherem Blut wurde PCR-amplifiziert unter Verwendung eines 2-Enzymsystems. Die Verwendung von ALF™Express DNA Sequencer wurde als hilfreich bei der genetischen Typisierung größerer Bevölkerungsgruppen angesehen. Statistische Analysen wurden mit POPGENE- und DISPAN-Programmen durchgeführt. Ergebnisse: Insgesamt wurden acht Allele mit Repeats zwischen 2 und 9 beobachtet. Das Allel 4 war unter allen fünf Populationen vorherrschend, passend zu Daten von anderen Völkern dieser Erde. Ein seltenes Allele 9 wurde ausschließlich bei den Marathas gefunden. Die beobachtete Heterozygotie war niedrig und reichte von 0,38 bis 0,54, während andere Parameter wie der Gehalt an Information betreffend Polymorphismus (Polymorphic Information Content) und die Unterscheidbarkeit (Power of Discrimination) mäßige Ausprägungen zeigten. Die Populationen waren bei Prüfung unter Hardy–Weinberg-Erwartungen im genetischen Äquilibrium. Zusammenfassung: Die hier vorgenommene Schätzung der Allelhäufigkeit für DRD4 wird zur Entwicklung einer informativen Datenbasis für diesen funktionell bedeutsamen locus beitragen. Dies wird sich als hilfreich für die Untersuchung der Beziehung zwischen genetischen Faktoren und der Pathogenese von Krankheiten in der Indischen Bevölkerung erweisen und wird Bedenken berücksichtigen hinsichtlich möglicher Beeinflussung von Ergebnissen aufgrund ethnischer Durchmischung. Resumen. Antecedentes: El gen D4 del receptor de la dopamina humana (DRD4) contiene una repetición en tándem de 48 pares de bases (pb) en el tercer exón y muestra alelos que varían entre 2 y 11 repeticiones. El gen muestra un elevado nivel de expresión en el córtex pre-frontal del cerebro y se ha señalado la asociación de alelos particulares de este locus con varios trastornos neuro-psiquiátricos y de la personalidad. Objetivo: El presente estudio informa sobre la distribución de frecuencias alélicas en el polimorfismo de repetición en tándem de número variable (VNTR) del locus DRD4, en cinco poblaciones étnicas de la India. Esta información es fundamental en el campo de la farmacogenética para los estudios sobre susceptibilidad a enfermedades y de asociación. Sujetos y métodos: Se tiparon 332 individuos adultos sanos, no emparentados, procedentes de cinco grupos étnicos, los Konkanastha, Brahmins, Marathas, Ezhavas, Nairs y Musulmanes. El ADN genómico, extraído de sangre periférica, se amplificó mediante PCR utilizando un sistema bi-enzimático. Se comprobó que el uso del secuenciador de ADN ALF™Express era útil para genotipar poblaciones a gran escala. Los análisis estadísticos se realizaron utilizando los programas POPGENE y DISPAN. Resultados: Se observó un total de ocho alelos que oscilaban entre 2 y 9 repeticiones. El alelo 4 fue el predominante en las cinco poblaciones, lo que era consistente con los datos de otras poblaciones del mundo. Se detectó un alelo 9 raro exclusivamente entre los Marathas. La heterozigosidad observada era baja, oscilando entre 0,38 y 0,54, mientras otros parámetros como el Contenido de Información Polimórfica (Polymorphic Information Content) y el Poder de Discriminación (Power of Discrimination) mostraron valores moderados. Las poblaciones estaban en equilibrio genético cuando se las testó bajo las condiciones de Hardy-Weinberg. Conclusión: Las estimaciones de las frecuencias alélicas para el gen DRD4 proporcionadas en este estudio, contribuirán al desarrollo de una base de datos informativa sobre este locus funcionalmente relevante. Esto será útil cuando se estudie la asociación entre los factores genéticos y la patogénesis de la enfermedad en poblaciones indias, y para tratar la inquietud por los resultados sesgados de asociación debidos a las mezclas de población.

Molecular Understanding of Growth Inhibitory Effect from Irradiated to Bystander Tumor Cells in Mouse Fibrosarcoma Tumor Model

Even though bystander effects pertaining to radiation risk assessment has been extensively studied, the molecular players of radiation induced bystander effect (RIBE) in the context of cancer radiotherapy are poorly known. In this regard, the present study is aimed to investigate the effect of irradiated tumor cells on the bystander counterparts in mouse fibrosarcoma (WEHI 164 cells) tumor model. Mice co-implanted with WEHI 164 cells γ-irradiated with a lethal dose of 15 Gy and unirradiated (bystander) WEHI 164 cells showed inhibited tumor growth, which was measured in terms of tumor volume and Luc+WEHI 164 cells based bioluminescence in vivo imaging. Histopathological analysis and other assays revealed decreased mitotic index, increased apoptosis and senescence in these tumor tissues. In addition, poor angiogenesis was observed in these tumor tissues, which was further confirmed by fluorescence imaging of tumor vascularisation and CD31 expression by immuno-histochemistry. Interestingly, the growth inhibitory bystander effect was exerted more prominently by soluble factors obtained from the irradiated tumor cells than the cellular fraction. Cytokine profiling of the supernatants obtained from the irradiated tumor cells showed increased levels of VEGF, Rantes, PDGF, GMCSF and IL-2 and decreased levels of IL-6 and SCF. Comparative proteomic analysis of the supernatants from the irradiated tumor cells showed differential expression of total 24 protein spots (21 up- and 3 down-regulated) when compared with the supernatant from the unirradiated control cells. The proteins which showed substantially higher level in the supernatant from the irradiated cells included diphosphate kinase B, heat shock cognate, annexin A1, angiopoietin-2, actin (cytoplasmic 1/2) and stress induced phosphoprotein 1. However, the levels of proteins like annexin A2, protein S100 A4 and cofilin was found to be lower in this supernatant. In conclusion, our results provided deeper insight about the damaging RIBE in an in vivo tumor model, which may have significant implication in improvement of cancer radiotherapy.

Population Genetic Analysis among Five Indian Population Groups Using Six Microsatellite Markers

Genetic variation at six tetranucleotide microsatellites (HUMTHO1, HUMVWA, F13A01, D3S1359, D12S66, and D12S67) has been determined in five endogamous ethnic population groups of India belonging to two major linguistic families. The populations analyzed were Konkanastha Brahmins and Marathas (Maharashtra state) from the Indo-Aryan linguistic family and Nairs, Ezhavas, and Muslims (Kerala state) from the Dravidian family. All six loci show high gene diversity, ranging from 0.63 ± 0.04 to 0.84 ± 0.02. The average GST value observed was 1.7%, indicating that the differences between the populations account for less than 2% of the diversity, while the genetic variation is high within the five population groups studied (>98%). The phylogenetic tree fails to show any clear cluster. The absence of any cluster along with low average GST is suggestive of substantial genetic similarity among the studied populations, in spite of clear geographical, linguistic, and cultural barriers. This similarity indicates either a greater gene flow between these groups or, alternatively, may reflect a recent evolution for them, considering that the Indian caste system evolved only about 3000 years ago.

Role of ATM in bystander signaling between human monocytes and lung adenocarcinoma cells

The response of a cell or tissue to ionizing radiation is mediated by direct damage to cellular components and indirect damage mediated by radiolysis of water. Radiation affects both irradiated cells and the surrounding cells and tissues. The radiation-induced bystander effect is defined by the presence of biological effects in cells that were not themselves in the field of irradiation. To establish the contribution of the bystander effect in the survival of the neighboring cells, lung carcinoma A549 cells were exposed to gamma-irradiation, 2Gy. The medium from the irradiated cells was transferred to non-irradiated A549 cells. Irradiated A549 cells as well as non-irradiated A549 cells cultured in the presence of medium from irradiated cells showed decrease in survival and increase in γ-H2AX and p-ATM foci, indicating a bystander effect. Bystander signaling was also observed between different cell types. Phorbol-12-myristate-13-acetate (PMA)-stimulated and gamma-irradiated U937 (human monocyte) cells induced a bystander response in non-irradiated A549 (lung carcinoma) cells as shown by decreased survival and increased γ-H2AX and p-ATM foci. Non-stimulated and/or irradiated U937 cells did not induce such effects in non-irradiated A549 cells. Since ATM protein was activated in irradiated cells as well as bystander cells, it was of interest to understand its role in bystander effect. Suppression of ATM with siRNA in A549 cells completely inhibited bystander effect in bystander A549 cells. On the other hand suppression of ATM with siRNA in PMA stimulated U937 cells caused only a partial inhibition of bystander effect in bystander A549 cells. These results indicate that apart from ATM, some additional factor may be involved in bystander effect between different cell types.

Population data of two minisatellite loci (D1S80 and D17S5) among five distinct ethnic groups of India.

Population Data of Two Minisatellite Loci (D1S80 and D17S5) Among Five Distinct Ethnic Groups of India

Distribution of allele frequencies for two short tandem repeats (HUMTH01 and F13A01) among five Indian population groups.

POPULATION: Populations studied include two groups from the state of Maharashtra, namely Konkanasthas and Marathas, and three groups from the state of Kerala, namely Nairs, Ezhavas, and Muslims. All the five groups are endogamous ethnic groups representing two geographically, linguistically, and culturally distinct Western and Southern regions of India. A total of 205 unrelated healthy donors for HUMTH01 and 227 individuals for F13A01 were analyzed.

Indian population data for two tetrameric short tandem repeat loci:vWA and D3S1359

POPULATION: Five anthropologically distinct population groups from two broad geographical areas of India were analyzed: Konkanasthas and Marathas from Western India (state of Maharashtra), and Nairs, Ezhavas, and Muslims from Southern India (state of Kerala). A total of 241 healthy adult volunteers for vWA and 194 individuals for D3S1359 were studied.

Allelic Variation at ACTBP2 Microsatellite for Two Indian Tribal Groups

POPULATION: Two tribal populations, Bison Horn Maria (N=49) and Muria (N=52) from Bastar district in Central India.

STR polymorphism among two tribal populations of India

Two tribal populations of India, Bison Horn Maria and Muria from Bastar district of Madhya Pradesh in Central India were studied for DNA polymorphisms at tetranucleotide short tandem repeat (STR) loci (F13A01 and HUMvWA). A total of 63 random adult individuals for F13A01 locus and 53 samples for HUMvWA were analyzed in the present study.

Characterization of TP53 Microsatellite Locus Among Selected Ethnic Populations of India

POPULATION A total of 253 individuals belonging to five ethnic populations of India were analyzed for pentanucleotide microsatellite TP53. These included Konkanasthas and Marathas (from Maharashtra, western India) representing Indo-Aryan lineage and Ezhavas, Nairs and Muslims (from Kerala, southwest India) representing Indo-Dravidian lineage. To the best of our knowledge, allele frequency data at TP53 microsatellite locus exists only for German Caucasians (1,2), Northern Portuguese (3) and West African from S. Tomé e Príncipe (4); the present study is the first report on Asian populations.