In-house reverse transcriptase polymerase chain reaction for detection of SARS-CoV-2 with increased sensitivity.

As the COVID-19 infection continues to ravage the world, the advent of an efficient as well as the economization of the existing RT-PCR based detection assay essentially can become a blessing in these testing times and significantly help in the management of the pandemic. This study demonstrated an innovative and rapid corroboration of COVID-19 test based on innovative multiplex PCR. An assessment of optimal PCR conditions to simultaneously amplify the SARS-CoV-2 genes E, S and RdRp has been made by fast-conventional and HRM coupled multiplex real-time PCR using the same sets of primers. All variables of practical value were studied by amplifying known target-sequences from ten-fold dilutions of archived positive samples of COVID-19 disease. The multiplexing with newly designed E, S and RdRp primers have shown an efficient amplification of the target region of SARS-CoV-2. A distinct amplification was observed in 37 min using thermal cycler while it took 96 min in HRM coupled real time detection using SYBR green over a wide range of template concentrations. Our findings revealed decent concordance with other commercially available detection kits. This fast HRM coupled multiplex real-time PCR with SYBR green approach offers rapid and sensitive detection of SARS-CoV-2 in a cost-effective manner apart from the added advantage of primer compatibility for use in conventional multiplex PCR. The highly reproducible novel approach can propel extended applicability for developing sustainable commercial product besides providing relief to a resource limited setting.

Protein Profile of Human Saliva as a Predictive and Prognostic Tool for OSCC in Tamol Chewer's Population in Assam.

OBJECTIVE: To identify potential proteomic salivary biomarker in tamol chewers and comparing it to healthy and Oral squamous cell carcinoma cases. METHODS: A total of fifty unstimulated saliva samples were collected from the healthy volunteers, tamol chewers (without tobacco), and OSCC patients referred to North-East cancer Hospital, Jorabat, Assam, India. The 2-D gel analysis and western blotting were performed to analyze protein profiling. RESULTS: The identified proteins were serum albumin, HSP (Heat shock protein) 27, gamma actin, SCC (Squamous cell carcinoma) 1, and Annexin A4. All the proteins were associated with OSCC development when their values were compared with those of normal healthy subjects. HSP27 was subjected to further validation using western blotting methods. An increase of 18.39% (Serum Albumin), 15.04% (gamma actin), 14.01% (SSC 1), and 20.22% (ANX4) were observed in Tamol chewers when compared with healthy control subjects. CONCLUSION: Our results revealed that the identified salivary proteins have a positive association with OSCC development. Profiling of these saliva proteomes especially HSP (Heat shock protein) 27 as a potential biomarker for OSCC detection in the high-risk population is recommended.

Expression Analysis of Serum microRNA-34a and microRNA-183 in Hepatocellular Carcinoma

Background/objective: HCC is a multistep process starting from chronic hepatitis that progress through cirrhosis to HCC. MicroRNA expression level was found to be deregulated in HCC. To find out whether the expression level of miR-34a and miR-183 was deregulated in HCC compared to controls without HCC. Methods: Real time quantitative PCR was done to find out the miRNA expression level in terms of Ct value followed by statistical analysis. Results: Over-expression of miR-183 and under-expression of miR-34a in HCC was detected. All changes in expression level of miR-34a and miR-183 were found to be due to HCC compared to controls without HCC. So both miR-34a and miR-183 were suitable to differentiate HCC from Cirrhosis and chronic hepatitis with an efficient diagnostic power of sensitivity, specificity and expression level. But they might not have any role in patients' survival. Conclusion: miR- 34a and miR-183 might be considered as potential markers of HCC screening molecule in addition to other approved panel of marker. Our study warrants further expression level study.

Detection of HBV Genotype C in Hepatocellular Carcinoma Patients from North East India: a Brief Report

Background and Objectives: Newer genotypes of HBV have been reported from India. This study was aimed to determine the circulating genotypes of HBV in hepatocellular carcinoma patients from three different geographical locations of India. Methods: 141 HBV related HCC cases were included from three different hospitals across the country. Genotyping of HBV was performed by PCR using type specific primers specially designed in 70 cases. Samples of interest were confirmed by direct sequencing of the precore/core region of HBV genome. Results: Genotypes could be detected in 40 (57.14%) out of the 70 HBV DNA positive HCC cases by type specific primers. HBV genotype D was documented in 20 (50%), genotype A in 10 (25.0%) and genotype C in 10 (25.0%) of these HCC cases. Genotype C of HBV was detected only in the samples from North East India. No significant difference was observed for the biochemical profile. Conclusion: Although Genotype D is the major HBV genotype in India followed by A, detection of HBV genotypes C in HCC patients indicates a changing epidemiology of the virus in India that may require region based management of the virus.

Polymorphisms in Heat Shock Proteins A1B and A1L (HOM) as Risk Factors for Oesophageal Carcinoma in Northeast India.

BACKGROUND: To investigate polymorphisms in heat shock proteins A1B and A1L (HOM) and associated risk of oesophageal carcinoma in Northeast India. MATERIALS AND METHODS: The study includes oesophageal cancer (ECA) patients attending general outpatient department (OPD) and endoscopic unit of Gauhati Medical College. Patients were diagnosed based on endoscopic and histopathological findings. Genomic DNA was typed for HSPA1B1267 and HSPA1L2437 SNPs using the polymerase chain reaction with restriction fragment length polymorphisms. RESULTS: A total of 78 cases and 100 age-sex matched healthy controls were included in the study with a male: female ratio of 5:3 and a mean age of 61.4±8.5 years. Clinico-pathological evaluation showed 84% had squamous cell carcinoma and 16% were adenocarcinoma. Dysphagia grades 4 (43.5%) and 5 (37.1%) were observed by endoscopic and hispathological evaluation. The frequency of genomic variation of A1B from wild type A/A to heterozygous A/G and mutant G/G showed a positive association [chi sq=19.9, p= <0.05] and the allelic frequency also showed a significant correlation [chi sq=10.3, with cases vs. controls, OR=0.32, p≤0.05]. The genomic variation of A1L from wild T/T to heterozygous T/C and mutant C/C were found positively associated [chi sq= 7.02, p<0.05] with development of ECA. While analyzing the allelic frequency, there was no significant association [chi sq= 3.19, OR=0.49, p=0.07]. Among all the risk factors, betel quid [OR =9.79, Chi square= 35.0, p<0.05], tobacco [OR = 2.95, chi square=10.6, p<0.05], smoking [OR=3.23, chi square=10.1, p<0.05] demonstrated significant differences between consumers vs. non consumers regarding EC development. Alcohol did not show any significant association [OR= 1.34, chi square=0.69, p=0.4] independently. CONCLUSIONS: It can be concluded that the present study provides marked evidence that polymorphisms of HSP70 A1B and HSP70 A1L genes are associated with the development of ECA in a population in Northeast India, A1B having a stronger influence. Betel quid consumption was found to be a highly significant risk factor, followed by smoking and tobacco chewing. Although alcohol was not a potent risk factor independently, alcohol consumption along with tobacco, smoking and betel nut was found to contribute to development of ECA.

Role of aflatoxin B1 as a risk for primary liver cancer in north Indian population.

OBJECTIVES: The present study was designed to determine whether aflatoxin B1 (AFB1) exposure has any role to play in hepatocellular carcinoma (HCC) patients from northern India. DESIGN AND METHODS: A total of 266 HCC patients and 251 patients of chronic liver disease without-HCC were enrolled into the study. All samples were screened for serological markers for hepatitis B and C infections and levels of AFB1 in food and urine samples. RESULTS: A threefold (OR=3.43) and five-fold (OR=5.47) increased risk of HCC was observed amongst HBV infection and AFB1-levels in food and urine samples, respectively. However, a non-significant risk was observed with respect to HCV infection (OR=1.27) and alcohol consumption (OR=1.18). A threefold (OR=3.15) increased risk of HCC was observed amongst cases of non-viral etiology with respect to urinary AFB1. CONCLUSION: The data provides an exposure and disease risk information for establishing intervention studies to diminish the impact of aflatoxin exposure in Indian population.

Genetic polymorphism of glutathione S transferases M1 and T1 in Indian patients with hepatocellular carcinoma.

OBJECTIVE: Our aim was to evaluate whether the association of GSTM1/T1 gene polymorphisms modifies the risk of Hepatocellular carcinoma (HCC) and what is its correlation with other predisposing risk factors like alcohol intake, cigarette smoking and hepatitis B and C infections. STUDY DESIGN/SETTING: It was a case-control study, included 254 HCC cases compared with 525 hospital-based age and sex matched cases of chronic liver disease without HCC as controls from Indian population. The GSTM1 and GSTT1 genotypes were detected using conventional multiplex PCR method. RESULTS: In this case-control study, we observed a positive correlation between age, HBV and HCV infection, smoking habit of > 20 packs/year, alcohol consumption of > 100 g/day and risk of liver cancer. We found significantly increased risk associated with GSTM1 null genotype (OR = 3.49; 95% CI = 2.52-4.84) as well as GSTT1 null genotype (OR = 3.12; 95% CI = 2.19-4.45), respectively. However, an increased risk of HCC was observed among heavy drinkers with GSTM1 (OR = 2.01; 95% CI = 1.11-3.66). Further, cigarette smoking showed a non-significant association with GSTT1 (OR = 1.49; CI = 0.69-3.25). CONCLUSION: Our results suggest that the variants in low penetrance gene such as GSTM1 and GSTT1 are associated with an increased liver cancer risk. Further, an influence of GSTM1/T1 null genotypes may contribute in the etiology of HCC in patients with higher cigarette and alcohol consumption.

Hepatitis B virus BCP, Precore/core, X gene mutations/genotypes and the risk of hepatocellular carcinoma in India.

The study aims to characterize mutations of the HBV genome involving BCP, Precore/core and X regions and also defines HBV genotypes in patients of hepatocellular carcinoma (HCC). The study involved 150 HBV-related HCC cases and 136 HBV-related chronic liver disease patients without HCC as controls. HBV DNA was subjected to mutational analysis using SSCP technique, genotyping by RFLP, and direct nucleotide sequencing. HBV DNA was found in 58.7% (88/150) of the HCC cases and 74.3% (101/136) of controls. HBV mutants were observed in 44.3% of HCC cases and 43.2% of controls. HBV/D was prevalent amongst the patients and controls, followed by HBV/A. The prevalence of the TT1504 mutation in the X gene, the V1753 and T1762/A1764 mutations in the BCP region, and G1914 mutation in the core gene were significantly higher in the HCC group than in the non-HCC group. Multivariate analyses showed that the TT1504, V1753, A1762T/G1764A, and the G1914 mutations and the patient's age, sex, and HBeAg status increased the risk of HCC development significantly. Also, patients with HCC had lower levels of serum albumin, viral load, and platelet counts but higher values of alkaline phosphatase, alanine aminotransferase, aspartate aminotransferase, bilirubin, and Alpha feto-protein than those of controls (P < 0.001 for all comparisons). HBV/D was the predominant genotype associated with HCC cases seen in India. The presence of different types of HBV mutations, age, sex, HBeAg status, and viral load was found to increase significantly the risk of HCC development in India.