NUDT15 C415T variant compared with TPMT genotyping in predicting azathioprine-induced leucopenia: prospective analysis of 1014 inflammatory bowel disease patients in India.

BACKGROUND: Recent studies reported that Nudix Hydrolase 15(NUDT 15) gene variant (C415T) can better predict thiopurine induced leucopenia in Asian patients with inflammatory bowel disease (IBD) than thiopurine S-methyl transferase (TPMT). AIM: To evaluate the role of the NUDT variant compared with TPMT in predicting azathioprine induced leucopenia in Indian IBD patients. METHODS: Prospectively collected data of consecutive patients treated with azathioprine from a large IBD registry were analysed for side effects, discontinuation time, and initial and maximum dose tolerated. Genotyping of NUDT15 C415T (rs116855232; p.R139C) was carried out retrieving blood samples from bio-repository employing real time polymerase chain reaction with age and sex-matched healthy volunteers. The association of NUDT15 C415T with leucopenia (<3 × 109 /L) and neutropenia (<1.5 × 109 /L) was evaluated. TPMT genotyping was done in patients who developed leucopenia. RESULTS: Among 1014 patients (mean age 35.84 ± 12.74 years; 61% males; 54% ulcerative colitis, 44% Crohn's disease and 2% IBD-unclassified), 79 were excluded due to inadequate blood samples. Of the remaining 935, 81 (9%) developed leucopenia and 70 (7.5%) developed neutropenia. The variant "T" allele [heterozygous (CT) and homozygous (TT) versus wild type (CC)] was associated with a 19-fold higher odds (OR19.35, 95% CI11.55-32.42; P < 0.0001) of leucopenia and 21-fold higher odds of neutropenia (OR21.41, 95% CI12.25-37.41). There was significant difference in median dose tolerated between CC, CT and TT (1.35, 1.38 and 0.92 mg/kg body weight, respectively) (P = 0.037) and median duration of therapy (18, 15 and 10 months for CC/CT/TT) (P = 0.003). NUDT15 genotype was an independent risk factor for leucopenia (hazard ratio (HR): CT 11.31, 95% CI6.85-18.03, P < 0.0001 and TT 31.283, 95% CI14.76-66.30 compared to CC) and neutropenia (HR: CT 13.04, 95% CI7.65-22.22, P < 0.0001 and TT 43.39, 95% CI20.21-92.68 compared to CC). The sensitivities for predicting leucopenia and neutropenia by number of mutant NUDT 15 alleles based on additive predictive model were 66.67% and 70% with a receptor operator characteristic curve area under curve value of 0.791 and 0.807, respectively. Among patients with leucopenia, only 6.2% were heterozygous and none were homozygous for TPMT variants. CONCLUSION: NUDT15 variant genotyping appears to be a better predictor for azathioprine-induced leucopenia in an Indian population than TPMT with high accuracy and can be useful in optimizing azathioprine dosage.

PRSS1 (R122H) mutation in an Indian family with low penetrance is associated with pancreatitis phenotype.

Mutations in PRSS1 gene namely R122H and N29I cause hereditary pancreatitis. They are autosomal dominant with a high penetrance (80%) reported in North American, North-east Asian, and North European ethnicities. However, the mutations are reportedly absent in Indian, African, and South American ethnicities. We report here for the first time a family from India that is positive for R122H mutation in the PRSS1 gene. The proband is symptomatic with chronic pancreatitis, however, the father although heterozygous for R122H is asymptomatic.

Hereditary Persistence of Alpha-Fetoprotein Is Associated with the -119G>A Polymorphism in AFP Gene.

Alpha-fetoprotein (AFP) is a glycoprotein that is produced by the liver and yolk sac during fetal development. Its levels are usually raised in malignant conditions. Hereditary persistence of AFP (HPAFP) is a rare benign condition with elevated levels of AFP. It is inherited in a dominant mode with complete penetrance and is usually not associated with any clinical disability. We report two individuals with elevated levels of AFP harboring the -119G>A polymorphism in the AFP gene. A genetic screening to rule out variants in the AFP gene is advised in cases with unexplained persistent AFP levels to avoid inappropriate treatment and surgical options.

Microsatellite instability and promoter hypermethylation in colorectal cancer in India.

Microsatellite instability (MSI) is an important factor in tumor development and is a hypermutable phenotype caused by the loss of DNA mismatch repair activity. It is important to identify tumors with microsatellite instability as the patients have a better prognosis and differ with response to chemotherapy. Limited data are available on the incidence of MSI in Indian colorectal cancers (CRCs). The objectives of this study were to identify the extent of MSI in Indian CRC patients below 50 years and to determine promoter methylation status of hMLH1 and hMSH2 in relation to MSI. A total of 450 patients were diagnosed with CRC, out of which 91 individuals were recruited as per Bethesda guidelines and were tested for instability by the NCI-recommended Bethesda panel (BAT25, BAT26, D2S123, D5S346, and D17S2720) using labeled primers. The fragments were separated and analyzed on a Beckman GeXP sequencer. Promoter methylation status was determined by restriction enzyme digestion and PCR. MSI (high and low) was seen in 48.4% (44/91) of CRC patients, out of which microsatellite instability-high (MSI-H) was detected in 13.2% (12/91) and microsatellite instability-low (MSI-L) in 35.2% (32/91) and the rest were microsatellite stable (MSS), 51.6% (47/91). Majority of the MSI-H tumors were adenocarcinomas (10/12), in the rectum (8/12), and moderately or poorly differentiated (12/12). Promoter hypermethylation was seen in 75% of the MSI-H, 56.24% of MSI-L, and only 23.4% of MSS individuals. MSI (high and low) was associated with 48.4% of CRC patients, and a significantly higher proportion of promoter hypermethylation of hMLH1 and hMSH2 genes was associated with instable tumors.