Molecular basis of X-linked non-specific mental retardation

Mental retardation (MR) is a common disorder, affecting 1-3% of the total population. This condition results from failure to develop cognitive abilities and intelligence level appropriate for the age group. Mental retardation is basically a clinically as well as etiologically heterogeneous type of condition and both genetic and non-genetic factors have been found to be involved. There are more than 1000 entries in Online Mendelian Inheritance in Man (OMIM) database under the name of mental retardation. In recent years 15 genes for X linked non-specific mental retardation have been identified which provide important clues regarding molecular and cellular processes involved in signal transduction cascade in central nervous system. Recent advancements in identification and characterization of X-linked non-specific mental retardation genes have been discussed in this review. Understanding of the molecular pathways of disease causing genes would be helpful in developing effective therapeutic approaches for mental retardation.

Targeting the hedgehog pathway for gallbladder cancer therapy?

Gallbladder carcinoma is a fatal malignancy of hepatobiliary tract that is generally diagnosed at advanced stages of cancer because of its asymptomatic nature. Advanced GBC tumors are unresectable with poor prognosis. Improvement in GBC patient care requires better understanding of the biological signaling pathways and application of newly discovered drugs for cancer therapy. Herein, we discuss the possibilities and challenges in targeting the hedgehog pathway in gallbladder cancer therapy based on recent developments in the area.

Carrier detection in non-deletional Duchenne/Becker muscular dystrophy families using polymorphic dinucleotide (CA) repeat loci of dystrophin gene

BACKGROUND & OBJECTIVES

Carrier detection and prenatal diagnosis is of great importance for families with one or more sons affected with Duchenne/Becker muscular dystrophy (D/BMD). In about 35-40 per cent of these patients, the causative mutation does not involve gross rearrangement in the structure of dystrophin gene. In these non-deletional families, genetic counselling can be provided only by linkage analysis. The aim of the present study was to determine the carrier status of female relatives in north Indian families with non-deletional D/BMD using highly polymorphic intragenic dinucleotide (CA) repeat markers.

METHODS

Six short tandem repeats (STRs) spanning 5' (1), central (4) and 3' regions of the dystrophin gene were used to analyse 14 unrelated families comprising 68 individuals with 12 female siblings at risk of being carriers.

RESULTS

Five female siblings inherited at risk STR haplotype, six inherited normal haplotype and one had meiotic recombination. The intragenic recombinations were observed in three families at the central region STR loci and in one family between the proximal and central regions of the gene.

INTERPRETATION & CONCLUSIONS

Our study suggested that at least 6 STR markers spanning 5', central and 3' regions of the dystrophin gene are essential to ascertain one or more informative loci and to rule out recombinations in non-deletional D/BMD families for carrier analysis.

Molecular diagnosis in haemophilia A

Haemophilia A is the commonest cause of X-linked inherited bleeding disorder. Due to inadequate medical facility for management of the disease, the DNA based genetic diagnosis has assumed great importance. Ideally, the direct detection of mutations is the most accurate and reliable approach for carrier detection and prenatal diagnosis. However, mutation detection is possible only in limited number of cases. In majority of haemophiliacs, no common mutation is easily identifiable. The limitation has been over come by the use of linkage-based analysis using polymorphic DNA markers in the factor VIII gene. Some of these markers can be identified by restriction enzymes and are called RFLP markers. Other markers are a class of short tandem repeats sequences which result in differences in the number of CA repeats in different individuals. The combined use of these markers has made it possible to identify carriers and provide prenatal diagnosis in upto 95% of families having affected individuals. Therefore, the recurrence of the disease can be prevented to a great extent in the haemophilia A affected families.

Alterations of p53 gene in gallbladder cancer patients of North India

BACKGROUND

Mutations in p53 gene are found in a majority of human malignancies and usually occur in the exons 5, 6, 7 and 8. Mutated p53 protein is more stable and gets accumulated in the cells that induce the host to develop anti-p53 antibodies in sera of cancer patients.

AIM

This study is aimed to observe the frequency and nature of mutations in exons 5-8 of p53 gene and to evaluate its correlation with prevalence of serum p53 antibodies in Indian patients with gallbladder cancer (GBC).

METHODS

Mutation studies were done in cancer tissues obtained from 62 patients with proven GBC (40 cytologically proven cases and 22 resected gallbladder cancer tissues) by polymerase chain reaction (PCR), restriction fragment length analysis (RFLP) and single strand conformation polymorphism (SSCP). Presence of serum p53 antibodies was determined using highly specific enzyme linked immunosorbent assay (ELISA) kit in 50 patients with GBC and 30 patients of cholelithiasis. Clinicopathologic characteristics of these patients were given attention.

RESULTS

Antibodies to p53 protein was present in the serum in 34% (17/50) of GBC patients and in 3.3% (1/30) patients with cholelithiasis (p < 0.018). RFLP failed to detect common mutations in the exons 5- 8 of the p53 gene in 62 samples. Using SSCP analysis we could detect frameshift mutation in p53 gene in 2 of 22 (9.1%) GBC cases. Mutated samples were sequenced and found to have insertion of adenine at codon 271 (GAG) in exon 8 region.

CONCLUSION

Our results show that 1//3rd of the north Indian patients with GBC have antibodies to p53 protein. The commonest identifiable alteration in the p53 gene was a frameshift mutation at codon 271.

Organic anion transporter protein (OATP1B1) encoded by SLCO1B1 gene polymorphism (388A>G) & susceptibility in gallstone disease

BACKGROUND & OBJECTIVES

Organic anion transport protein 1B1 (OATP1B1) is a major transporter protein for bile salt uptake in the enterohepatic circulation of bile salts. As the role of SLCO1B1 gene (encodes OATP1B1 or liver specific transporter-1) 388 A>G polymorphism in susceptibility towards gallstone disease is unclear the prevalence of this polymorphism in healthy north Indian population was investigated.

METHODS

Peripheral venous blood of 270 unrelated northern Indian patients with symptomatic gallstone disease and 270 unrelated healthy control subjects was screened for SLCO1B1 gene 388 A>G polymorphism by PCR-RFLP method and genotyping was done on 12 per cent polyacrylamide gel. The cross-sectional data on accrual of cases and controls were collected and odds ratio with 95 per cent CI calculated as for case-control design.

RESULTS

Allele frequencies of 388 G were 45 per cent in gallstone cases and 44 per cent in controls with no statistical significance. Genotype frequencies in gallstone cases and controls for, genotype AA were 30 and 32 per cent; AG: 51 and 47 per cent and GG: 16 and 21 per cent respectively. No significant association of any allele or genotype with gallstone disease was found.

INTERPRETATION & CONCLUSION

Although the prevalence of SLCO1B1 gene 388A>G polymorphism in north Indian population in high, yet this polymorphism does not appear to play a significant role in susceptibility to gallstone formation.

Polymorphism of GSTM1 and GSTT1 genes in prostate cancer: a study from North India

BACKGROUND

Glutathione-S-transferases (GSTs) are active in the detoxification of wide variety of endogenous or exogenous carcinogens. The genetic polymorphisms of GSTM1 and GSTT1 genes have been studied earlier to evaluate the relative risk of various cancers. AIM, SETTING AND DESIGN: In the present study, we examined the association of the GSTM1 and GSTT1 gene polymorphisms with sporadic prostate cancer patients in north Indian population.

MATERIAL AND METHODS

This case control study was undertaken over a period of 24 months and included 103 prostate cancer patients and 117 controls; both patients and controls originated from northern part of India. The GSTT1 and GSTM1 genotypes were identified by multiplex PCR in peripheral blood DNA samples.

STATISTICAL ANALYSIS

Difference in genotype prevalence and association between case and control group were assessed by the Chi square and Fisher Exact tests.

RESULTS

Frequencies of null genotypes in GSTT1 and GSTM1, was 11% (13/117) and 30% (35/117) respectively in control individuals. The frequencies of GSTT1 and GSTM1 null genotypes in prostate cancer patients were 34% (35/103) and 53% (55/103) respectively.

CONCLUSION

Our study demonstrates that the null genotypes of GSTT1 and GSTM1 are substantially at higher risk for prostate carcinoma as compared to the normal healthy controls. The GSTT1 and GSTM1 null genotypes did not show significant association with tobacco usage in prostate cancer patients. However, the null genotypes were significantly stratified in 50-60 year-old patients when incidence of prostate cancer is high.

Serotonin transporter gene (SLC6A4) polymorphism in patients with irritable bowel syndrome and healthy controls

BACKGROUND

Polymorphisms in serotonin re-uptake transporter (SERT or SLC6A4) gene may play role in disturbance in gut function in irritable bowel syndrome (IBS). The aim of this study was to evaluate the association between SLC6A4 polymorphism of SERT-P and serotonin (5-hydroxytryptamine, 5-HT) concentration in IBS as compared with controls.

METHODS

150 patients with IBS (Rome-III criteria) and 252 controls were subjected to SLC6A4 genotyping. 5-HT was measured in the rectal biopsy of patients only.

RESULTS

Patients and controls were age and gender-matched. Patients were classified into D-IBS: 79 (52%), C-IBS: 52 (35%) and A-IBS: 19 (13%). SLC6A4 polymorphism differed in IBS and controls [genotypes s/s, 89 (59%), l/s, 44 (29%), and l/l, 17 (12%) vs. s/s, 92 (37%), l/s, 114 (45%), and l/l, 46 (18%), p<0.001]. SLC6A4 s/s genotype was commoner in D-IBS than C-IBS, A-IBS and controls (p<0.001). 5-HT level was higher in D-IBS than A-IBS and C-IBS (154.7±37.1 vs. 112.4±24.6 vs. 104.3±23.7-pmol/mL, p<0.001) and in s/s than l/s and l/l genotypes (151.1±37.3 vs. 105.0±20.9 vs. 100.9±28.0-pmol/mL, p<0.001). IBS with s/s genotype more often had abdominal pain than l/s and l/l [78/89 (87.6%) vs. 19/44 (43%) vs. 5/17 (29%), p<0.001]. 5-HT level was higher among IBS patients with abdominal pain and diarrhea than without (142.9±39.4 vs. 108.4±28.9-pmol/mL, p<0.001) and (140.2±41.3-pmol/mL vs. 121.3±35.0-pmol/mL, p=0.003).

CONCLUSION

The frequency of SLC6A4-polymorphism and higher levels of 5-HT were significantly associated with IBS, particularly in patients with diarrhea and abdominal pain, suggesting that SLC6A4 is a potential candidate gene involved in the pathogenesis of IBS.

Pathophysiology and genetics of obesity

Obesity, a global problem, is a multifactorial disorder. The factors are environmental, metabolic and genetic and their interaction with each other regulates the body weight. Imbalance in either of the factors may be responsible for weight gain. With advancement of research techniques in the last decade, genetic studies have been undertaken for several different causative mutations involving obesity loci on different chromosomes. Monogenic and polygenic obesity has been observed however, polygenic forms are more common. So far more than 200 genes in mouse and more than 100 genes in humans have been identified which result in phenotypes that affect body weight regulation. In spite of this knowledge, the field of obesity has still not been explored extensively. There remain a lot of lacuna regarding causes and treatment of obesity. Challenges are still there to identify the exact cause of weight gain and the use of current knowledge for development of anti-obesity drugs targeted for body weight regulation. In this review, we have explained neuropathophysiologic regulation of feeding behaviour and some aspects of obesity-genetics especially with single nucleotide polymorphism of selected candidate genes and their functional aspects mainly in monogenic obesity.

Fight against cancer in countries with limited resources: the post-genomic era scenario

The enormous advances in science and technology in the 20th century have facilitated the process of globalization with the aim of a better quality of life for all. Paradoxically, the gap between the rich and the poor, for both nations and people, is constantly widening. The actual trends in human genome research are leading towards promising genomic medicine, but it will be expensive and inaccessible for many. Also, it may not offer a quick fix "cure" for various types of cancers. The biggest challenge before the clinicians now is the management of the rising incidence of cancer in developing countries, with little prospect of more resources becoming available to fight the disease. The death rate from cancer in the developing countries is set to rise at least 3-fold by the year 2025 largely due to the increased life expectancy, containment of infectious diseases and changing lifestyles. It is estimated that about 50% of cancers are curable if they are detected early and treated appropriately. Screening has a major role in early diagnosis. However, in the developing world around 80% of cancer patients have late stage incurable disease when they are diagnosed. Moreover, in a developing country like India, about 70% of the population obtain medical help from private practitioners. Nearly half of those who seek medical help utilize alternative and traditional systems of medicine. Appalling poverty, poor hygiene and complex social dynamics, pose major hurdles in this regard. Many in the private sector who call themselves doctors have no medical degree. By 2030 tobacco is expected to kill 10 million people worldwide, out of which 70% of the deaths will occur in the developing countries. Control of usage of tobacco has still not achieved a conducive atmosphere. It is now realized that the research information and knowledge generated in the west may neither be relevant nor applicable to developing countries, due to differences in social and cultural attitudes, lifestyles and lack of sophisticated technologies. Though the sequencing of the human genome will have a major impact on the prevention, diagnosis, treatment, monitoring, and outcome of cancer, the cancer scenario in the developing countries for the next 20 years is likely to be more or less the same, rather than presenting a radically different picture. Cancer awareness and screening programs for early detection thus should be continue to be given utmost attention.

A clinical and genetic study of spinal muscular atrophy

AIMS

This study evaluates clinical, electromyography (EMG) and genetic analysis of consecutive patients with spinal muscular atrophy (SMA) in a tertiary care adult neurology practice in India.

METHODS

Consecutive patients with SMA attending the neurology out patient department during 2001-2003 were included. They were subjected to a detailed clinical examination, nerve conduction and EMG and muscle biopsy. Clinically patients were classified into generalised and segmental SMA. SMN gene deletion study was carried out in all the patients.

RESULTS

There were 15 patients with type III and type IV SMA and 15 with segmental SMA (Hirayama disease). The age ranged between 5 and 23 years in type III SMA, 33-50 years in type IV SMA and 16-30 years in Hirayama disease (HD). The latter was found exclusively in males. Family history was observed in 1 patient each in all the groups. In SMA III mother and brother were affected, in SMA IV two siblings and in HD one brother had similar disease. One type III SMA family was associated with deafness and one type IV family had strong association with maturity onset diabetes in young. The EMG was characterised by lack of fibrillations in all type III and IV SMA patients except 1 whereas in HD, 11 out of 15 had fibrillations suggesting ongoing denervation. The EMG was suggestive of reinnervation in generalised SMA in both upper and lower limb muscles where as these abnormalities were restricted to C7-T1 mytomes in HD. Muscle biopsy in 10 patients with generalised SMA revealed group atrophy in all, and loss of fascicular architecture in 3, clumping of nuclei in 7 and hypertrophic fibers in 4. SMN1 gene deletion was present in 3 patients with type III but none in type IV and HD.

CONCLUSION

SMN gene deletion was positive in 33% type III SMA whereas it was negative in type IV and HD. Presence of HD only in males may be consistent with X-linked disorder.

CYP4F2 1347 G > A & GGCX 12970 C > G polymorphisms: frequency in north Indians & their effect on dosing of acenocoumarol oral anticoagulant

BACKGROUND & OBJECTIVES

CYP4F2 and γ-glutamyl carboxylase (GGCX) have small but significant roles in the maintenance dose of coumarinic oral anticoagulants (COAs). CYP4F2 1347 G > A and GGCX 12970 C > G polymorphisms have been used in the pharmacogenetic dosing algorithms of warfarin for Caucasians and Chinese populations. India has a large population with multiple ethnic groups but there are no reports about the frequencies of these polymorphisms in north Indians. In the present study, we aimed to find out the allelic frequencies of CYP4F2 1347 G > A and GGCX 12970 C > G polymorphisms in a north Indian population and relate these to daily maintenance drug dose requirements of COA.

METHODS

CYP4F2 1347 G > A and GGCX 12970 C > G polymorphisms were genotyped by polymerase chain reaction - restriction fragment length polymorphism (PCR-RFLP) protocols and Taqman SNP discrimination assays in healthy volunteers (n=102) and patients (n=225) receiving acenocoumarol, an oral anticoagulant, after cardiac valve replacement surgery.

RESULTS

In healthy volunteers, the allele frequencies for CYP4F2 1347 G > A and GGCX 12970 C > G were 43.14 and 1.43 per cent, respectively. No significant differences in mean weight normalized doses of acenocoumarol were found for these CYP4F2 and GGCX genotypes. Binary logistic regression analysis revealed no significant association of any of the genotypes or alleles with the dosing phenotypes for both the SNPs.

INTERPRETATION & CONCLUSIONS

We report distinct frequencies of CYP4F2 1347 G > A and GGCX 12970 C > G polymorphisms in north Indians but these polymorphisms did not have significant bearing on maintenance dose of acenocoumarol oral anticoagulant in cardiac valve replacement patients.

Improving cancer care in India: prospects and challenges

The World Cancer Report, a 351 - page global report issued by International Agency for Research on Cancer (IARC) tells us that cancer rates are set to increase at an alarming rate globally (Stewart and Kleiues 2003). Cancer rates could increase by 50 % to 15 million new cases in the year 2020. This will be mainly due to steadily aging populations in both developed and developing countries and also to current trends in smoking prevalence and the growing adoption of unhealthy lifestyles. The report also reveals that cancer has emerged as a major public health problem in developing countries, matching its effect in industrialized nations. Healthy lifestyles and public health action by governments and health practitioners could stem this trend, and prevent as many as one third of cancers worldwide. In a developing country such as India there has been a steady increase in the Crude Incidence Rate (CIR) of all cancers affecting both men and women over the last 15 years. The increase reported by the cancer registries is nearly 12 per cent from 1985 to 2001, representing a 57 per cent rise in India's cancer burden. The total number of new cases, which stood at 5.3 lakhs Care lakh is 100,000 in 1985 has risen to over 8.3 lakhs today. The pattern of cancers has changed over the years, with a disturbing increase in cases that are linked to the use of tobacco. In 2003, there were 3.85 lakhs of cases coming under this category in comparison with 1.94 lakhs cases two decades ago. Lung cancer is now the second most common cancer among men. Earlier, it was in fifth place. Among women in urban areas, cancer of the uterine cervix had the highest incidence 15 years ago, but it has now been overtaken by breast cancer. In rural areas, cervical cancer remains the most common form of the disease (The Hindu 2004).

Detection of gene deletion in patients of Duchenne muscular dystrophy/Becker muscular dystrophy using polymerase chain reaction

Polymerase chain reaction (PCR) was used to study the presence of gene deletion (the most prominent type of mutations) in some families afflicted by Duchenne muscular dystrophy/Becker muscular dystrophy (DMD/BMD). The results clearly demonstrate deletion in the central part of the DMD gene in two of the three families studied. This information can be useful for genetic counselling with particular reference to prenatal diagnosis and carrier analysis.

DNA mismatch repair, microsatellite instability and cancer

Mismatch (MMR) repair system plays a significant role in restoration of stability in the genome. Mutations in mismatch repair genes hamper their activity thus bring about a defect in mismatch repair (MMR) mechanism thereby conferring instability in the microsatellite sequences of both the coding and non-coding regions of the genome. Mutated mismatch repair genes result in the expansion or contraction of microsatellite sequence and confer microsatellite unstable or replication error positive phenotype. Hypermethylation of promoter regions of some of the MMR genes also causes inactivation of these genes and thus contribute to MSI. Microsatellite instability is an indicator of MMR deficiency and is a prime cause of varied tumorogenesis.

Evaluation of microsatellite instability in tumors of central nervous system: A pilot study

Microsatellite instability (MSI) characterized by alterations at simple repetitive genomic sequences is a distinct mechanism in tumorogenesis. Central nervous system (CNS) tumors have been reported to exhibit MSI, indicator of defective mismatch repair system with controversies. The present study was undertaken to examine sixteen primary brain and two spinal tumors for MSI at six mono: BAT-26, BAT-40, BAX, TGFßRII, IGFIIR and hMSH3 and four dinucleotide loci: D2S123, D9S1851, D9S283 and D18S58. Polymerase chain reaction (PCR) was done to amplify tumour and blood DNA, analyzed on 8% denaturing Polyacrylamide gel followed by autoradiography. Out of 18 CNS tumors examined, 39% exhibited MSI at BAT-26, BAT-40, D9S1851, D9S283 and D18S58 in tumoral DNA. However, no alteration was observed at BAX, TGFßRII, IGFIIR, hMSH3 and D2S123 loci. Low incidence of MS1-high hypothesizes role of MSI in evolution of CNS tumors but not in cancer initiation or progression.