KRAS and BRAF genetic alterations in lung cancer: A case - control study.

CONTEXT: Lung cancer (LC) is one of the most critical neoplastic abnormalities, having globally a high mortality rate. Knowledge about its genetic mutations and their association with clinically pathological features of LC is very important. Here, we describe the epidemiological molecular study of genetic mutations in KRAS and BRAF genes and their relationship with the demographic and clinical characteristics of Pakistani patients with lung adenocarcinoma. AIM: To analyze the mutations of KRAS and BRAF in LC patients among Pakistani population. SETTINGS AND DESIGN: The study has been carried out at universities and health institutes of Islamabad, Pakistan. METHODS AND MATERIAL: Deoxyribonucleic acid (DNA) was extracted from the patient samples by using the standard protocol and amplified by using the specific primers. Later on, the Polymerase Chain Reaction (PCR) products were examined with the help of single stranded conformational polymorphism (SSCP). STATISTICAL ANALYSIS: Relationship between KRAS, BRAF mutations, and LC risk was accessed by conditional logistic regression using SPSS version 24.0. Results were illustrated by odds ratio (OR), 95% confidence interval (CI), and P value. RESULTS: LC is more common in male population and smoking is one of the leading risk factors for (p < 0.0001) LC. KRAS and BRAF mutations were found to be contributing factors toward LC development and showed statistically significant results along with conformation through computational analysis. CONCLUSIONS: It can be concluded that smoking is lethal and cancer causing. The concomitant mutations found in KRAS and BRAF were infrequent, and they probably have a very unusual effect on the clinical management of Pakistani patients with lung adenocarcinoma.

Gamma rays and sodium azide induced variations in bio-physiological and agronomical traits in linseed (Linum usitatissimum L.).

Linseed is a valuable oilseed crop with huge therapeutic importance due to its high content of omega-3 fatty acids in the form of Alpha-linolenic acid (ALA). It is a self-pollinated crop with a low-yielding potential that restricts its improvement endeavors. To overcome low-yielding potential, individual and combination treatments of gamma rays and sodium azide were employed in widely grown linseed varieties. The results revealed a dose-dependent decline in seed germination, seedling height, pollen fertility, chlorophyll, and carotenoid contents and a dose-independent decline in carbonic anhydrase activity. Bio-physiological parameters decreased substantially in combination treatments compared to individual treatments of gamma rays and sodium azide. In contrast, lower doses of gamma rays, sodium azide, and their combinations effectively increased mean values of yield and yield-attributing traits in a few putative mutants. Such putative mutants represent a valuable genetic resource that could be used in future breeding programs for the genetic improvement of linseed and related medicinal plants.

Exploring the experiences and expectations of trainee representatives in medical specialties: A qualitative study in the West Midlands, UK.

Introduction: Despite its importance, there is a paucity of evidence describing the role and responsibilities of trainee representatives. Aim: This study explored key stakeholders' experiences and expectations of the trainee representative role. Method: All eligible individuals in the West Midlands Deanery's School of Medicine were invited to participate in an interview exploring their experiences and expectations of the trainee representative role. Recurring themes were identified through thematic analysis using NVivo12 software. Results: Five themes-Support for trainee representatives, Deanery events for trainee representatives, Roles and responsibilities of trainee representatives, Representation and recruitment, and Benefits of being a trainee representative-were identified. Formalising appointments to such roles and providing induction and information on key responsibilities were highlighted as steps to minimise the gap. Conclusion: Trainee representative positions allow trainees to explore leadership roles; however, further work is needed to improve the resources to support the professional development of trainee representatives.

Efficacy of insula deep repetitive transcranial magnetic stimulation combined with varenicline for smoking cessation: A randomized, double-blind, sham controlled trial.

BACKGROUND: Current smoking cessation treatments are limited in terms of efficacy, particularly with regards to long term abstinence. There is a large amount of evidence implicating the insula in nicotine addiction. OBJECTIVE: To examine the efficacy of bilateral repetitive transcranial magnetic stimulation (rTMS) directed to the insular cortex with the H11 coil, relative to sham stimulation, on smoking abstinence and smoking outcomes in smokers who are receiving standard varenicline treatment. METHODS: This randomized, double-blind, sham controlled trial recruited 42 participants who were randomized to receive either active (n = 24) or sham (n = 18) high frequency rTMS directed to the insula (4 weeks), while receiving varenicline treatment (12 weeks). The primary outcome was 7-day point prevalence abstinence at the end of 12 weeks. RESULTS: Smokers in the active group had significantly higher abstinence rates than those in the sham group (82.4% vs. 30.7%, p = 0.013) at the end of treatment (Week 12). Secondary outcome measures of abstinence rate at the end of rTMS treatment (Week 4), abstinence rate at 6 months, and smoking outcomes (e.g., craving, withdrawal) showed no significant differences between groups. No differences were found in adverse events reported between the groups. CONCLUSION: This study provides evidence of the potential benefit of having a combined treatment for smoking cessation using insula rTMS with the H11 coil and varenicline. Maintenance rTMS sessions and continuation of varenicline for those in abstinence may induce longer-term effects and should be considered in future studies.

CYP2C19*17 association with higher plasma 4-hydroxy tamoxifen in Pakistani (estrogen-positive) breast cancer patients.

Breast cancer (BC) continues to be the most common cancer in the women worldwide. Since estrogen receptor (ER)-positive BC accounts for the majority of newly diagnosed cases, endocrine therapy is advised to utilize either tamoxifen (Tam) or aromatase inhibitors. The use of Tam as a monotherapy or in conjunction with an aromatase inhibitor following two or three years of endocrine therapy has long been recommended. When used adjuvantly, Tam medication reduces BC mortality and relapses, while it extends survival times in metastatic BC when used in conjunction with other treatments. Unfortunately, the efficiency of Tam varies considerably. This study was conducted to explore the influence of genetic polymorphisms in CYP2C19 gene on Tam's pharmacogenetics and pharmacokinetics in estrogen-positive BC patients. Data from healthy, unrelated individuals (n = 410; control group) and ER-positive BC patients (n = 430) receiving 20 mg of Tam per day were recruited. Steady-state plasma concentrations of Tam and its three metabolites were quantified using the high-performance liquid chromatography in the patients. The CYP2C19 polymorphisms were genotyped using an Amplification Refractory Mutation System-Polymerase Chain Reaction (ARMS-PCR) approach. More than 65% of healthy individuals were extensive metabolizers (*1/*1) for CYP2C19, whereas more than 70% of ER-positive BC patients were rapid and ultrarapid metabolizers (*1/17*, *17/17*). The polymorphism CYP2C19*17 is significantly associated with higher 4-hydroxytamoxifen (4-OH-Tam). Patients with the *17/*17 genotype exhibited 1- to 1.5-fold higher 4-OH-Tam, which was also high in patients with the *1/*2 and *2/*2 genotypes.

Estimating disparities in breast cancer screening programs towards mortality, case fatality, and DALYs across BRICS-plus.

BACKGROUND: Numerous studies over the past four decades have revealed that breast cancer screening (BCS) significantly reduces breast cancer (BC) mortality. However, in BRICS-plus countries, the association between BCS and BC case fatality and disability are unknown. This study examines the association of different BCS approaches with age-standardized mortality, case-fatality, and disability-adjusted life years (DALYs) rates, as well as with other biological and sociodemographic risk variables, across BRICS-plus from a national and economic perspective. METHODS: In this ecological study applying mixed-effect multilevel regression models, a country-specific dataset was analyzed by combining data from the Global Burden of Disease study 2019 on female age-standardized BC mortality, incidence, and DALYs rates with information on national/regional BCS availability (against no such program or only a pilot program) and BCS type (only self-breast examination (SBE) and/or clinical breast examination (CBE) [SBE/CBE] versus SBE/CBE with mammographic screening availability [MM and/or SBE/CBE] versus SBE/CBE/mammographic with digital mammography and/or ultrasound (US) [DMM/US and/or previous tests] in BRICS-plus countries. RESULTS: Compared to self/clinical breast examinations (SBE/CBE) across BRICS-plus, more complex BCS program availability was the most significant predictor of decreased mortality [MM and/or SBE/CBE: - 2.64, p < 0.001; DMM/US and/or previous tests: - 1.40, p < 0.001]. In the BRICS-plus, CVD presence, high BMI, second-hand smoke, and active smoking all contributed to an increase in BC mortality and DALY rate. High-income and middle-income regions in BRICS-plus had significantly lower age-standardized BC mortality, case-fatality, and DALYs rates than low-income regions when nationwide BC screening programs were implemented. CONCLUSIONS: The availability of mammography (digital or traditional) and BCS is associated with breast cancer burden in BRICS-plus countries, with regional variations. In light of high-quality evidence from previous causal studies, these findings further support the preventive role of mammography screening for BCS at the national level. Intervening on BCS related risk factors may further reduce the disease burden associated with BC.

Comprehensive in silico analyses of flavonoids elucidating the drug properties against kidney disease by targeting AIM2.

Kidney disorders are among the most common diseases and there is a scarcity of effective treatments for chronic kidney disease. There has been a progressive improvement in specific flavonoids for protective effects against kidney diseases. Flavonoids inhibit the regulatory enzymes to control inflammation-related diseases. In the present study, a hybrid approach of molecular docking analyses and molecular dynamic simulation was followed by principal component analyses and a dynamics cross-correlation matrix. In the present study, the top-ranked five flavonoids were reported, and the maximum binding affinity was observed against AIM2. Molecular docking analyses revealed that Glu_186, Phe_187, Lys_245, Glu_248, Ile_263, and Asn_265 are potent residues against AIM2 for ligand-receptor interactions. Extensive in silico analyses suggested that procyanidin is a potential molecule against AIM2. Moreover, the site-directed mutagenesis for the reported interacting residues of AIM2 could be important for further in vitro analyses. The observed novel results based on extensive computational analyses may be significant for potential drug design against renal disorders by targeting AIM2.

Insula deep rTMS and varenicline for smoking cessation: A randomized control trial study protocol.

Background: Current approved therapies for smoking cessation have modest long-term effects for abstinence. The insular cortex has been identified by preclinical and clinical studies as a critical target for addiction treatment. Insula functions can be modulated non-invasively using brain stimulation. It is unknown if deep repetitive transcranial magnetic stimulation (rTMS) of the insula can improve smoking cessation of smokers trying to quit using varenicline. Methods: This will be a randomized, double-blind, sham-controlled clinical trial with 50 nicotine dependent smokers looking to quit. They will be randomly assigned to receive either active (10 Hz) or sham insula deep rTMS. Deep rTMS will be administered for 4 weeks (5 days/week). All participants will receive open label varenicline for 12 weeks. The primary outcome measure will be the 7-day point prevalence abstinence at the end of 12 weeks. The secondary outcomes will be Fagerström Test of Nicotine Dependence, Minnesota Nicotine Withdrawal Scale, Tiffany Questionnaire of Smoking Urges, expired carbon monoxide measurements, cigarettes smoked per day, point prevalence abstinence at end of 4 weeks, prolonged and continuous abstinence at 6 months. The measures will be collected throughout the 3-month treatment period as well as at the 6-month follow up. Discussion: This trial will test for the first time the impact of deep insula rTMS on smoking cessation in smokers treated with varenicline. This trial will use an H-coil specific to the insula, while previous studies have targeted both the insula and prefrontal cortex. This trial will inform on the utility to combine insula deep rTMS with varenicline to improve smoking abstinence rates. Clinical Trial Registration: Trial registered at https://clinicaltrials.gov/ct2/show/NCT04083144 (Identifier: NCT04083144).

Epidemiological and sociodemographic transitions of female breast cancer incidence, death, case fatality and DALYs in 21 world regions and globally, from 1990 to 2017: An Age-Period-Cohort Analysis.

Introduction: Breast cancer (BC) is the most widely studied disease due to its higher prevalence, heterogeneity and mortality. Objectives: This study aimed to compare female BC trends among 21 world regions and globally over 28 year of data and to assess the association between sociodemographic transitions and female BC risks. Methods: We used Global burden of disease study data and measure the female BC burden according to 21 world regions and sociodemographic indices (SDI). Age-period-cohort (APC) analysis was used to estimate time and cohort trend of BC in different SDI regions. Results: By world regions, age-standardised rate of female BC incidence were high in high-income-North America (ASR, 92.9; (95 %UI, 89.2, 96.6)), Western Europe (84.7; (73.4, 97.2)) and Australia (86; (81.7, 90.2)) in 2017. Whereas this rate was significantly increased by 89.5% between 1990 and 2017 in East Asia. We observed negative association between SDI and death, and DALYs in 25th and below percentiles of death and DALYs for the worldwide regions. Further, there was observed a strong negative correlation between SDI and case fatality percent (r2017 = -0.93; r1990 = -0.92) in both 2017 and 1990 worldwide and highest case fatality percentage was observed in Central Sub-Saharan Africa. Overall, the risk of case-fatality rate tends to decrease most noticeably in high middle SDI countries, and the reduction of the risk of case-fatality rate in the recent cohort was the lowest in the low SDI countries. Conclusions: Remarkable variations exist among various regions in BC burden. There is a need to reduce the health burden from BC in less developed and under developing countries, because under-developed countries are facing higher degree of health-related burden. Public health managers should execute more classified and cost-effective screening and treatment interferences to lessen the deaths caused by BC, predominantly among middle and low SDI countries having inadequate healthcare supplies.

Evaluation of lifestyle risk factor differences in global patterns of breast cancer mortality and DALYs during 1990-2017 using hierarchical age-period-cohort analysis.

BACKGROUND: Statistical evidence on breast cancer (BC) burden related to health and lifestyle risk factors are valuable for health policy-making. This study aimed to compare the trends in BC mortality and disability adjusted life years (DALYs) attributable to various health and life style risk factors among different world's regions according to sociodemographic index (SDI). METHODS: We extracted the age-standardized and age-specific rate of mortality and DALYs of women BC during 1990-2017 using the comparative risk assessment framework of the 2017 global burden of disease (GBD) study. We performed hierarchical age-period-cohort analysis to estimate age- and time-related trends, and effect of interactions between different risk factors on BC risk. RESULTS: During 1990-2017, the age-standardized rate of mortality and DALYs of women BC was increasing in less developed and under developing regions. The risk factor alcohol use [RR 51.3(95%CI 17.6-149.7)] and smoking [5.9(2.0-17.3)] were significantly highly contributor to increased mortality risk in high SDI region. Whereas in the low-SDI region, the greater mortality risk was observed in alcohol use [6.9(2.4-17)] and high FPG [2.7(1.5-3.1)]-related deaths. The adjusting for individual age, period, and risk factor effects, the significant interaction effect between metabolic risk factors and older ages were observed in all SDI regions and globally as well. However, an increasing cohort effect of alcohol, high fasting plasma glucose (FPG) and smoking-related death, and DALYs was observed during 1960 to 1985 cohorts among low-SDI regions. CONCLUSIONS: The age-standardized rates of mortality and DALYs due to BC has been increasing in low-SDI region. Alcohol consumption, high body mass index (BMI), high FPG, and smoking are potential BC risk factors particularly in older ages that leading to adverse disease outcomes. Therefore, rapid aging and prevalence of these prospective risk factors may strengthen the increasing mortality and DALYs of BC in low-SDI region. Hence, preventive measure along with strict action against concerned BC risk factors should be taken to reduce the disease burden specifically among lower-SDI regions.

Attitude toward personal genomics: A nation-wide survey of public and professionals in Pakistan.

With the emergence of modern genetic testing and profiling techniques, it has become imperative to assess the general public awareness and attitudes toward such developments. The public's perspective and possible responses are necessary for planning commercial, legal, medical, or healthcare initiatives. The purpose of this study was to assess the perception of the general public and professionals about the personal genome testing and genetic profiling. A questionnaire-based survey was conducted to investigate the attitudes of 2954 adults (56.4% male and 43.6% female) from more than 120 different educational, research, and professional organizations of Pakistan. The aim of the study was to assess interest in genomic testing. The findings of this survey will feed into the larger Genome Projects in Pakistan and will be helpful for the national bioethical committee, healthcare agencies, diagnostic companies, and other institutions for making policy decisions.

Statistical analysis of COVID-19 infection caused by environmental factors: Evidence from Pakistan.

BACKGROUND: Coronavirus disease 2019 (COVID-19) has become a severe public health problem around the globe. Various epidemiological, statistical, and laboratory-based studies have shown that the role of temperature and other environmental factors has important influence in the transmission of coronaviruses. Scientific research is needed to answer the questions about the spread and transmission of the infection, whether people could be avoided from being infected with COVID-19 in next summer. AIM: We aim to investigate the association of daily average temperature, daily average dew point, daily average humidity, daily average wind speed, and daily average pressure with the infection caused by this novel coronavirus in Pakistan. KEY FINDINGS: First, we check the correlation between environmental factors and daily infected cases of COVID-19; among them, temperature and dew point have positive linear relationship with daily infected cases of COVID-19. The thought-provoking findings of the present study suggested that higher temperature and dew point can contribute to a rise in COVID-19 disease in four provinces of Pakistan, possible to genome modifications and viral resistance to harsh environment. Moreover, it is also observed that humidity in Punjab and Sindh, and wind speed in Balochistan and Khyber Pakhtunkhwa have influenced the spreading of daily infected COVID-19 cases. SIGNIFICANCE: Current study will serve as a guideline to develop understanding of environmental factors that influence COVID-19 spread, helping policymakers to prepare and handle a catastrophe resulting from this pandemic.

Referral indications for foetal echocardiography in a low resource setting.

OBJECTIVE: The aim of this study was to review primary indications for foetal echocardiography among pregnant women at a tertiary care center in a low resource setting. METHODS: A retrospective record review was conducted of all women who have had a foetal echocardiogram between January 2015 and December 2016 at The Aga Khan University Hospital, Karachi, Pakistan. Information regarding maternal clinical characteristics, anomaly scan findings, indications for echocardiography and findings on foetal echocardiogram (FE) was collected. RESULTS: The dataset included 1909 patients. Maternal comorbidities including maternal diabetes, (n=614, 47%) was the most common maternal indication, while multiple pregnancy (n=232, 38%) and intra-cardiac echogenic foci (n=168, 28%) was the most common foetal indication for referral. Major CHD was detected in 4.2% (n=81) of cases. In those with CHD, the most common indication for getting a FE was an abnormal 4-chamber (n=31, 38%) view on the screening obstetric ultrasound. CONCLUSIONS: Most of our patients were referred on the basis of indications that were not warranted based on international guidelines and very few had major CHD on FE. This emphasizes the need for justifying referrals for a resource intensive procedure such as FE.

Correlation of MSH2 exonic deletions and protein downregulation with breast cancer biomarkers and outcome in Pakistani women/patients.

Mismatch repair (MMR) pathway is one of the underlying mechanisms of predisposition to breast cancer (BC). The present study explored the association of MSH2 exonic deletions, respective survival analysis, protein structure prediction, transcription profiling, and expression analysis with BC risk. Genotyping analysis of 493 BC cases and 387 controls confirmed the association of two MSH2 exonic deletions, i.e., exon 3 (OR:6.4, CI = 3.4-12.1) and 9 (OR:7.8, CI = 4.1-14.8) with BC risk. In order to confirm the phenotypic-genotypic relationship, we have performed MSH2 transcriptomic (p < 0.05) and protein expression analysis (OR:30, CI = 4-230) which further confirmed its downregulation/loss in BC biopsy samples highlighting potential role in the onset of breast carcinogenesis. Additionally, we have presented that MSH2 mutations can alter the expression profile of other BC associated biomarkers like ER, PR, CK-7, GATA-3, and E-cadherin. Subsequently, the effect of exonic deletions on secondary structure of protein has shown missing of beta and alpha helices in their protein products via in-silico analysis. However, loss of exon 3 results in the altered core protein structure leading to dysfunction protein, possible cause of BC development. No association of MSH2 exonic deletions with survival statistics was observed conceivably due to the shorter follow-up time. Thus, our results at genetic, transcriptomic, and proteomic levels confirmed the downregulated MSH2, emphasizing its potential contribution in MMR mechanisms for breast tumorigenesis. In conclusion, MSH2 deficiency may cause breast cancer development and progression.

Possible Potential Outcomes from COVID-19 Complications on Testes: Lesson from SARS Infection.

Coronavirus infection disease-2019 (COVID-19) gained worldwide fame after deadly outbreak in China and its subsequent spread to many countries. So far, COVID-19 is not fully contained, and new cases are arising on daily bases in various countries. Due to zoonotic nature and human-to-human spread, COVID-19 is considered pandemic with more causalities in developing countries. Full genome analysis revealed its resemblance with severe acute respiratory syndrome (SARS) virus with minor variation in non-structural proteins. Both viruses use the common angiotensin converting enzyme (ACE2) receptor to attach to the epithelial cells of the target organs. Currently, COVID-19 patients are treated with drugs that are used for lungs infections. However, ACE2 has high expression in other human organs such as kidney and testes. Thus, it is assumed that, like SARS, it may have adverse effects on other vital organs, which have dominant expression of ACE2. In testis, SARS affected patients displayed peritubular fibrosis, extensive germ cell disruption, damage of blood-testis barrier integrity and more frequent occurrence of apoptosis. Here, we critically discuss the possible adverse effects of COVID-19 on the testes of patients along with future precautions to overcome the complications of reproductive organs. Key Words: COVID-19; SARS; ACE2, Testes.

Unraveling the Epidemiology, Geographical Distribution, and Genomic Evolution of Potentially Lethal Coronaviruses (SARS, MERS, and SARS CoV-2).

SARS CoV appeared in 2003 in China, transmitted from bats to humans via eating infected animals. It affected 8,096 humans with a death rate of 11% affecting 21 countries. The receptor binding domain (RBD) in S protein of this virus gets attached with the ACE2 receptors present on human cells. MERS CoV was first reported in 2012 in Middle East, originated from bat and transmitted to humans through camels. MERS CoV has a fatality rate of 35% and last case reported was in 2017 making a total of 1,879 cases worldwide. DPP4 expressed on human cells is the main attaching site for RBD in S protein of MERS CoV. Folding of RBD plays a crucial role in its pathogenesis. Virus causing COVID-19 was named as SARS CoV-2 due its homology with SARS CoV that emerged in 2003. It has become a pandemic affecting nearly 200 countries in just 3 months' time with a death rate of 2-3% currently. The new virus is fast spreading, but it utilizes the same RBD and ACE2 receptors along with furin present in human cells. The lessons learned from the SARS and MERS epidemics are the best social weapons to face and fight against this novel global threat.