Covid-19: a novel challenge to human immune genetic machinery

COVID-19 also called corona virus emerged in China in December 2019. This turned into a global pandemic in a short period of time. Covid-19 is a novel strain of corona virus that was not seen earlier in human beings. It is important to study the molecular structure of Covid-19 so as to aid in the development of therapeutic measures. Existing Covid-19 pandemic poses an extraordinary risk to health and healthcare systems worldwide. Corona viruses are made of single stranded RNA present within the coat proteins. The virus has a diameter of nearly 80–120 nm. Usually, Covid-19 presents with the signs and symptoms of respiratory illness. Cough commonly dry cough, fever, associated with myalgias and sometimes breathing difficulties due to decrease in oxygen saturation rates are also present in these patients. Some people show fever with body aches, while some are relatively asymptomatic. Corona virus is primarily transmitted in humans through respiratory route and is highly contagious. Mostly old people and those having comorbid illnesses suffer most. After invading into the human body, the virus may lead to a sequence of processes such as viral invasion, replication, and programmed cell death, that is, apoptosis. To control and prevent this viral infection, we need to study the molecular aspects of Covid-19 in detail so as to design therapeutic agents as well as for vaccine formation. The micro-RNA is defined as the single-stranded noncoding RNA molecule. They have a length of about 22 nucleotides approximately and help in the post transcriptional regulation of gene expression. Micro RNAs regulate many types of cancers in addition to Covid-19 and other infections. Viral micro RNA is a newer type of mi-RNA and controls the host cell expression and viral target genes. This was completed by inducing micro-RNA cleavage, breakdown, translation, inhibition, or other mechanisms. The micro-RNAs of Covid-19 are explained to give an authoritative means to study this novel coronavirus. These control the host cell expression and also viral target genes by inducing micro-RNA cleavage, breakdown, translation, inhibition, and also other mechanisms.

Prevalence and prognostic relevance of BrafV600E mutation in colorectal carcinomas from Kashmir (North India) valley

Molecular studies have implicated mutant B-type Raf kinase (BRAFMut) of MAP-kinase signalling pathway in the pathogenesis of several cancers including colorectal cancer. Recently, the prognostic and therapeutic relevance of the most frequent BRAFV600E mutation also has been highlighted in colorectal carcinomas (CRC). Thus, the aim of this study was to investigate the prevalence of BRAFV600E mutation and to determine the correlation between this mutation and indicators of poor prognosis and outcome in patients with CRCs from Kashmir, North India. Here, we developed a highly sensitive technique, mutation allele-specific multiplex PCR (MASMP), for detection of BRAFV600E/BRAFc.1799T>A mutation, the results of which were confirmed by sequencing the product and compared to direct DNA sequencing. In total, BRAFV600E mutation status was analyzed in 57 colorectal tumour samples and an equal number of adjacent normal tissues. A high frequency of BRAFV600E mutation 21% (12/57) was identified in tumour tissues by MASMP compared to only 5.2% by direct DNA sequencing. Statistical analysis indicated that compared to BRAF-negative colorectal tumours, patients with BRAFV600E colorectal tumours were more likely to be >50 years old (61%) (P < 0.03). These tumours were more likely to be of clinical tumour stages III and IV (63%) (P < 0.04) with lymph node metastasis (52%) (P < 0.02) and characterised by a high-grade histology (63%) (P < 0.04). Colorectal patients harbouring BRAFV600E mutation experience more relapse/recurrence (52%) (P < 0.02). We, therefore, conclude that BRAFV600E mutation can be used as an indicator of poor prognosis to predict the outcome for CRC patients from Kashmir. MASMP proved to be a simple, sensitive and reliable technique for screening patients for BRAFV600E mutation. Testing for this mutation may be useful for selecting initial therapy mode and for follow-up monitoring in CRC patients.

Identification and characterisation of a novel heat shock protein 90 inhibitor ONO4140

Heat shock protein (Hsp) 90 is a key component of the super-chaperone complex that maintains functionally active conformation of various client proteins. Many of these client proteins regulate important nodal points in multiple signalling pathways that promote cancer cell growth and survival. Inhibitors of Hsp90, therefore, have the potential of functioning as anti-cancer agents with pleiotropic effects. Identification of novel Hsp90 inhibitors with more favourable pharmacological properties is a priority in cancer therapy. To achieve this goal, we screened a compound library using a biochemical assay based on refolding of denatured firefly luciferase. The assay revealed high sensitivity, reliability and reproducibility with a Z-factor of 0.81 ± 0.17. Six Hsp90 inhibitory compounds identified by this screening with IC50 values between 1.0 and 6 μM were further characterised for anti-proliferative activity by Cell Titer-Blue Cell Viability Assay using multiple tumour cell lines. Of particular interest was ONO4140 with lowest GI50 values in three different cancer cell lines viz; DU-145, BT-474 and K562 cell lines. This study also revealed that short-term exposure of tumour cells with ONO4140 is sufficient to inhibit the catalytic activity of Hsp90, evaluated through disruption of Hsp90-p23 association by immunoprecipitation. This short term exposure appears to initiate events like degradation of Hsp90 client proteins such as ErbB2/Her-2 and Akt with concomitant inhibition of survival signalling leading to the apoptotic death of tumour cells as seen by western blotting and Caspase Glow-3,7 assay. The study also reveals that apoptosis following Hsp90 inhibition with ONO4140 occurs via Caspase9-Caspase3 intrinsic apoptotic pathway, a process that is likely triggered by inactivation of Akt. In conclusion, we have identified a novel class of synthetic compounds which show potent Hsp90 inhibitory action in preclinical studies. The discovery of this novel class of synthetic Hsp90 inhibitors with simple chemical backbone allows us to conduct further structural modifications to improve their potency and pharmacokinetic properties for use in cancer therapy.

Evaluation of polymerase chain reaction for rapid diagnosis of clinically suspected tuberculous pleurisy

Pleural effusion is one of the commonest presentations of tuberculosis, the clinical manifestations being typically abrupt resembling bacterial pneumonia. Since delayed hypersensitivity is the underlying immune response, bacterial load is very low. Owing to these facts, tuberculous pleurisy as an extra-pulmonary disease poses a diagnostic dilemma. The conventional bacteriological methods rarely detect Mycobacterium tuberculosis in pleural fluid and are of limited use in diagnosis of tuberculous pleurisy. We evaluated the efficacy of polymerase chain reaction (PCR) in the diagnosis of tuberculous pleurisy by targeting the gene segment coding for MPB64 protein specific forMycobacterium tuberculosis. Based on the clinical criteria, 82 patients with lymphocytic exudative pleural effusion were included in the study. Patients were analyzed in two groups; one group consisting of 48 patients of tubercular pleural effusion confimed by various diagnostic procedures and another group of 34 patients comprising of non-tubercular pleural effusion. There were no false positive results by PCR and the specificity worked out to be 100%. Twenty two patients tested positive for Mantoux with a sensitivity of 45%. ZN-staining for AFB was found in samples from 15 patients (20% sensitivity). ADA was positive for 28 patients with a sensitivity of 53%. PCR was positive for 32/48 patients (67% sensitivity). Thus, PCR was found to be more sensitive than any other conventional method in diagnosis of clinically suspected tubercular pleurisy.

Comparison and agreement between venous and arterial gas analysis in cardiopulmonary patients in Kashmir valley of the Indian subcontinent

BACKGROUND

Arterial blood gas (ABG) analysis is routinely performed for sick patients but is fraught with complications, is painful, and is technically demanding.

OBJECTIVE

To ascertain agreement between the arterial and peripheral venous measurement of pH, pCO(2), pO(2), and bicarbonate levels in sick patients with cardiopulmonary disorders in the valley of Kashmir in the Indian subcontinent, so as to use venous gas analysis instead of arterial for assessment of patients.

SETTING

Sher-i-Kashmir Institute of Medical Sciences, Srinagar, Kashmir, a 650-bedded tertiary care hospital in North India located at an altitude of 1584 m.

METHODS

One hundred patients who required ABG analysis were admitted. Peripheral venous blood was drawn within 5 min of an ABG measurement, and the samples analyzed immediately on a point of care automated ABG analyzer. Finger pulse oximetry was used to obtain oxygen (SpO(2)) saturation. Data were analyzed using Pearson correlation and bias (Bland Altman) methods.

RESULTS

The venous measurements of pH, pCO(2), pO(2) and bicarbonate, and the digital oxygen saturation were highly correlated with their corresponding arterial measurements. Bland Altman plots demonstrated a high degree of agreement between the two corresponding sets of measurements with clinically acceptable differences. The difference in pO(2) measurements was, however, higher (-22.34 ± 15.23) although the arterial saturation and finger oximetry revealed a good degree of agreement with clinically acceptable bias.

CONCLUSION

Peripheral venous blood gas assessment in conjunction with finger pulse oximetry can obviate the routine use of arterial puncture in patients requiring ABG analysis.

Improved diagnosis of central nervous system tuberculosis by MPB64-Target PCR

Central nervous system (CNS) tuberculosis is a serious clinical problem, the treatment of which is sometimes hampered by delayed diagnosis. Clearly, prompt laboratory diagnosis is of vital importance as the spectrum of disease is wide and abnormalities of the cerebrospinal fluid (CSF) are incredibly variable. Since delayed hypersensitivity is the underlying immune response, bacterial load is very low. The conventional bacteriological methods rarely detect Mycobacterium tuberculosis in CSF and are of limited use in diagnosis of tuberculous meningitis (TBM). This double blind study was, therefore, directed to the molecular analysis of CNS tuberculosis by an in-house-developed PCR targeted for amplification of a 240bp nucleotide sequence coding for MPB64 protein specific for Mycobacterium tuberculosis. Based on the clinical criteria, 47 patients with CNS tuberculosis and a control group of 10 patients having non-tubercular lesions of the CNS were included in the study. Analyses were done in three groups; one group consisting of 27 patients of TBM, a second group of 20 patients with intracranial tuberculomas and a third group of 10 patients having nontubercular lesions of the CNS acted as control. There were no false positive results by PCR and the specificity worked out to be 100%. In the three study groups, routine CSF analysis (cells and chemistry), CSF for AFB smear and culture were negative in all cases. PCR was positive for 21/27 patients (77.7% sensitivity) of the first group of TBM patients, 6/20 patients (30% sensitivity) of the second group with intracranial tuberculomas were positive by PCR and none was PCR-positive (100% specificity) in the third group. Thus, PCR was found to be more sensitive than any other conventional method in the diagnosis of clinically suspected tubercular meningitis.

BRCA1 and TP53 mutation spectrum of breast carcinoma in an ethnic population of Kashmir, an emerging high-risk area

Breast cancer shows geographical variation in its incidence, even within areas of ethnic homogeneity. Kashmir valley (India), over past few years, witnesses an increase in incidence and occurrence of familial, early onset, and male breast cancer in its unexplored ethnic population. Here, we make a preliminary attempt to estimate the nature and frequency of BRCA1 and TP53 gene mutations of breast cancer patients from Kashmir. PCR-SSCP analysis followed by direct sequencing revealed the presence of only two germline intronic variations (c.199+67T>C and c.5396+187T>C) in BRCA1 gene in only 5.26% (2/38) patients while as 44% (11/25) of sporadic breast cancer patients harboured significant amount of somatic mutations in TP53 (p=0.0074; OR=0.053). The 17 mutations found in TP53 in 11 patients, comprised of 13 substitutions [11 single-base (9 transitions+2 transversions), 1 double-base and 1 complex] and four insertions. The 11 substitutions represent missense mutations, leading to aminoacid substitution while as rest two were silent mutations. The four insertions represented three frame-shifts and one non-sense mutation. The mutation effect data was found to be significant (p=0.0002). Significant amount of mutations were found in exon 6 (p=0.04; OR=0.273) and a combination of exons 6 and 7 (p=0.0145; OR=14.22) of TP53. Comparison of mutation profile with other ethnic populations and regions reflected both differences and similarities indicating co-exposure to a unique set of risk factors. The differences could be due to exposure to particular environmental carcinogens; different lifestyle, reproductive pattern; dietary or cultural practices of Kashmiri women that need further investigations. The infrequent presence of germline BRCA1 mutations in our study agree with the idea that a great proportion of moderate risk breast cancer population could be due to the susceptibility genes distinct from BRCA1. However, high frequency of somatic TP53 gene mutations implicates TP53 as a predominant factor for breast carcinogenesis in moderate risk ethnic Kashmiri population. The study also suggests TP53 as a potential molecular marker and prognostic tool, at least in a subset of sporadic breast tumors.