Mutational signatures in esophageal squamous cell carcinoma from eight countries with varying incidence

Esophageal squamous cell carcinoma (ESCC) shows remarkable variation in incidence that is not fully explained by known lifestyle and environmental risk factors. It has been speculated that an unknown exogenous exposure(s) could be responsible. Here we combine the fields of mutational signature analysis with cancer epidemiology to study 552 ESCC genomes from eight countries with varying incidence rates. Mutational profiles were similar across all countries studied. Associations between specific mutational signatures and ESCC risk factors were identified for tobacco, alcohol, opium and germline variants, with modest impacts on mutation burden. We find no evidence of a mutational signature indicative of an exogenous exposure capable of explaining differences in ESCC incidence. Apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like (APOBEC)-associated mutational signatures single-base substitution (SBS)2 and SBS13 were present in 88% and 91% of cases, respectively, and accounted for 25% of the mutation burden on average, indicating that APOBEC activation is a crucial step in ESCC tumor development.

Joint effect of diabetes and opiate use on all-cause and cause-specific mortality: the Golestan cohort study

BACKGROUND

Many diabetic individuals use prescription and non-prescription opioids and opiates. We aimed to investigate the joint effect of diabetes and opiate use on all-cause and cause-specific mortality.

METHODS

Golestan Cohort study is a prospective population-based study in Iran. A total of 50 045 people-aged 40-75, 28 811 women, 8487 opiate users, 3548 diabetic patients-were followed during a median of 11.1 years, with over 99% success follow-up. Hazard ratio and 95% confidence intervals (HRs, 95% CIs), and preventable death attributable to each risk factor, were calculated.

RESULTS

After 533 309 person-years, 7060 deaths occurred: 4178 (10.8%) of non-diabetic non-opiate users, 757 (25.3%) diabetic non-users, 1906 (24.0%) non-diabetic opiate users and 219 (39.8%) diabetic opiate users. Compared with non-diabetic non-users, HRs (95% CIs) for all-cause mortality were 2.17 (2.00-2.35) in diabetic non-opiate users, 1.63 (1.53-1.74) in non-diabetic opiate users and 2.76 (2.40-3.17) in diabetic opiate users. Among those who both had diabetes and used opiates, 63.8% (95% CI: 58.3%-68.5%) of all deaths were attributable to these risk factors, compared with 53.9% (95% CI: 50%-57.4%) in people who only had diabetes and 38.7% (95% CI: 34.6%-42.5%) in non-diabetic opiate users. Diabetes was more strongly associated with cardiovascular than cancer mortality. The risk of early mortality in known cases of diabetes did not depend on whether they started opiate use before or after their diagnosis.

CONCLUSIONS

Using opiates is detrimental to the health of diabetic patients. Public awareness about the health effects of opiates, and improvement of diabetes care especially among individuals with or at risk of opiate use, are necessary.

Hazards of cigarettes, smokeless tobacco and waterpipe in a Middle Eastern Population: a Cohort Study of 50 000 individuals from Iran

BACKGROUND

There is limited information about the hazards of cigarettes, smokeless tobacco and waterpipe in the Middle East. The aim of this study was to determine the association between different types of tobacco use and earlier death in the Golestan Cohort Study.

METHODS

The Study includes 50 045 adults (aged 40-75 years) from north eastern Iran. The baseline questionnaire (2004-2008) assessed information about use of cigarettes, chewing tobacco (nass) and waterpipe. To assess the use of each type of tobacco compared with never tobacco users, we used Cox regression models adjusted for age, socioeconomic status, area of residence, education and other tobacco used, and stratified by sex, ethnicity and opium use.

RESULTS

17% of participants reported a history of cigarette smoking, 7.5% chewing tobacco (nass) and 1.1% smoking waterpipe, and these figures declined in the later birth cohorts. During a median follow-up of 8 years, 4524 deaths occurred (mean age 64.8+9.9 years). Current (HR=1.44; 95% CI 1.28 to 1.61) and former (HR=1.35; 95% CI 1.16 to 1.56) cigarette smokers had higher overall mortality relative to never tobacco users. The highest cigarette-associated risk was for cancer death among current heavy smokers (HR=2.32; 95% CI 1.66 to 3.24). Current nass chewing was associated with overall mortality (HR=1.16; 95% CI 1.01 to 1.34), and there was a 61% higher risk of cancer death in people chewing nass more than five times a day. We observed an association between the cumulative lifetime waterpipe use (waterpipe-years≥28) and both overall (HR=1.66; 95% CI 1.11 to 2.47), and cancer mortality (HR=2.82; 95% CI 1.30 to 6.11).

CONCLUSIONS

Regular use of cigarettes, smokeless tobacco and waterpipe were associated with the risk of earlier death (particularly from cancer) in our cohort.

Mortality from respiratory diseases associated with opium use: a population-based cohort study

BACKGROUND

Recent studies have suggested that opium use may increase mortality from cancer and cardiovascular diseases. However, no comprehensive study of opium use and mortality from respiratory diseases has been published. We aimed to study the association between opium use and mortality from respiratory disease using prospectively collected data.

METHODS

We used data from the Golestan Cohort Study, a prospective cohort study in northeastern Iran, with detailed, validated data on opium use and several other exposures. A total of 50 045 adults were enrolled from 2004 to 2008, and followed annually until June 2015, with a follow-up success rate of 99%. We used Cox proportional hazard regression models to evaluate the association between opium use and outcomes of interest.

RESULTS

During the follow-up period, 331 deaths from respiratory disease were reported (85 due to respiratory malignancies and 246 due to non-malignant aetiologies). Opium use was associated with an increased risk of death from any respiratory disease (adjusted HR 95% CI 3.13 (2.42 to 4.04)). The association was dose-dependent with a HR of 3.84 (2.61 to 5.67) for the highest quintile of cumulative opium use versus never use (Ptrend<0.001). The HRs (95% CI) for the associations between opium use and malignant and non-malignant causes of respiratory mortality were 1.96 (1.18 to 3.25) and 3.71 (2.76 to 4.96), respectively.

CONCLUSIONS

Long-term opium use is associated with increased mortality from both malignant and non-malignant respiratory diseases.

Cloning the hbs gene from Bacillus subtilis and expression of the HBsu protein in Escherichia coli

BACKGROUND AND OBJECTIVES

Bacillus subtilis HBsu is a 10 kD heat-stable protein shown to be involved in binding to DNA and is encoded by the hbs gene. Large-scale production for biochemical analysis is achieved through cloning and expression of the recombinant protein.

MATERIALS AND METHODS

This gene was amplified from B. subtilis ATCC 6633 using PCR and cloned into pET28a (+) expression vector. The construct was used to transform Escherichia coli BL21 (DE3). The expression of the protein was induced by the addition of 1mM IPTG. To confirm the expression of the cloned gene, SDS-PAGE was carried out and production of an approximately 11 KD recombinant tagged protein was confirmed for the cloned hbs gene.

RESULTS AND CONCLUSION

The identity of the recombinant HBsu was verified and characterized by SDS-PAGE which can then be utilized for further applications.

Non-radioactive labeled probe preparation for hbs gene detection

Among some Bacillus species, a protein highly homologous to HU, classified HB and coded by hbs gene. According to the recent studies, the sequence of hbs gene just in one strain of Bacillus subtilis exists in gene bank (ATCC 23857). In this study, DNA from Bacillus subtilis ATCC 6633 was extracted and investigated by PCR. The PCR product was sequenced and shown to differ in just one nucleotide from B. subtilis ATCC 23857. Hence, it was chosen as reference and for the first time, used for non-radioactive labeled probe preparation. The PCR product in Bacillus subtilis with ATCC 6633 was labeled using non-radioactive DIG-labeled nucleotides and conditions of probe preparation and hybridization were optimized and checked it by Southern blotting.

Pulsed field gel electrophoresis & plasmid profile of Pseudomonas aeruginosa at two hospitals in Tehran, Iran

BACKGROUND & OBJECTIVE

Pseudomonas aeruginosa is a common cause of nosocomial infections and exhibits innate resistance to a wide range of antibiotics. This study was undertaken to determine the resistance patterns of P. aeruginosa isolates recovered from patients at two hospitals in Tehran, to investigate the presence of plasmids and to genetically characterize them by pulsed field gel electrophoresis (PFGE).

METHODS

The susceptibility of 104 isolates of P. aeruginosa to 13 different antibiotics was determined by agar disk diffusion method. The alkaline lysis method was used for plasmid extraction. PFGE technique was optimized for DNA fingerprinting of isolates.

RESULTS

The isolates showed resistance to 13 different antibiotics ceftizoxime (99%), lomefloxacin (94.3%), ceftazidime (59.6%), ticarcillin (50%), ceftriaxone (44.3%), cefoperazone (37.5%), tobramycin (34.6%), piperacillin and gentamicin (33.7%), carbenicillin (25%), amikacin (22%), ciprofloxacin (15.4%) and imipenem (2.9%). Plasmids were detected in 31 isolates (29.8%) that produced 15 different patterns. In total, 84 DNA banding patterns were detected by PFGE. The dominant PFGE type, Pattern A with 14 isolates was found at both hospitals. The remaining isolates were grouped in B, C, D and PF1-PF80. The majority of isolates with the identical plasmid profiles and resistance patterns produced closely related DNA fingerprints by PFGE.

INTERPRETATION & CONCLUSION

Isolates in pattern A were distributed widely at both hospitals and the environment. Absence of plasmids in majority of isolates indicated low typeability and discriminatory power of this technique.

Multidrug-resistant strains of Mycobacterium tuberculosis isolated from patients in Tehran belong to a genetically distinct cluster

Restriction fragment length polymorphism (RFLP) analysis was used to study the molecular epidemiology of tuberculosis (TB) in certain areas of Tehran. 120 isolates of Mycobacterium tuberculosis, including drug-resistant strains (n = 23), were analysed using polymorphic GC-rich sequence (PGRS) and IS6110 probes. There was considerable diversity among the strains cultured from patients from certain areas. The results of RFLP showed that multidrug resistant (MDR) isolates of M. tuberculosis in Tehran belong to a group of strains with low copies of IS6110 and PGRS. The degree of clustering was higher for the drug-resistant strains than for the susceptible ones (65% vs 20%). Based on the demographic data and results of RFLP, it appears that recent transmissions of TB from old patients have occurred in Tehran. However, drug-resistant TB in the city is mainly caused by strains that look different from those cultured from such patients. The majority of MDR isolates (85%) in this study contained a low copy number of IS6110 and PGRS in RFLP, and were mostly recovered from immigrants and refugees.