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.

Comparative In Silico Analysis and Functional Characterization of TANK-Binding Kinase 1-Binding Protein 1.

Protein modelling plays a vital role in the drug discovery process. TANK-binding kinase 1-binding protein 1 is also called an adapter protein, which is encoded by gene TBK1 present in Homo sapiens. It is found in lungs, small intestine, leukocytes, heart, placenta, muscle, kidney, lower level of thymus, and brain. It has a number of protein-binding sites, to which TBK1 and IKBKE bind and perform different functions as immunomodulatory, antiproliferative, and antiviral innate immunity which release different types of interferons. Our study predicts the comparative model of 3-dimensional (3D) structure through different bioinformatics tools that will be helpful for further studies in future. The reactivity and stability of these proteins were evaluated physicochemically and through domain determination and prediction of secondary structure using bioinformatics methods such as ProtParam, Pfam, and SOPMA, respectively. Robetta, an ab initio approach, I-TASSER, and AlphaFold was used for 3D structure prediction, and the models were validated using the SAVESv6.0 (PROCHECK) server. Conclusively, the best 3D structure of TBK1-binding protein 1 was predicted using Robetta software. After unveiling the 3D structure of the novel protein, we concluded that this structure will help us to find out its role other than in antiviral innate immunity and by producing torsion in its 3D structure researchers will be able to detect either this protein is involved in any disease or not because according to previous studies it was not associated with any disease.

Phylogenetic and sequencing analysis of Chikungunya virus strains from local Pakistani population.

OBJECTIVE: To outline the genotype of Chikungunya virus strains and to form their phylogenetic tree. METHODS: The cross-sectional study was conducted at the Armed Forces Institute of Pathology, Rawalpindi, Pakistan, from August 2016 to September 2017, and comprised suspected Chikungunya samples. The viral ribonucleic acid was extracted and amplified. The purified product was sequenced using Sanger dideoxy method. Phylogenetic tree was constructed. Sequences generated were checked for alignment with sequences reported globally. Structural prediction and analysis was performed using Phyre2 and the models were visualised in PyMol2.2. RESULTS: In the 11 suspected samples, 7(63.6%) were found to be positive for Chikungunya. Of them, 5(71.4%) sequences generated were found to be aligned with other full structural polyprotein sequences, having 99% similarity with amino acid sequences. CONCLUSIONS: The Chikungunya strains in the study belonged to the East/Central/South African genotype.

Biochemical spectrum of parathyroid disorders diagnosed at a tertiary care setting.

OBJECTIVE: To determine the clinical and biochemical pattern of parathyroid disorders in a tertiary care setting.. METHODS: The cross-sectional study was conducted at the Armed Forces Institute of Pathology, Rawalpindi, Pakistan, from September 2017 to February 2018, and comprised patients with suspected parathyroid disorders. A panel of biochemical tests were used for diagnosis of parathyroid disorders, which included parathyroid hormone levels, total calcium, ionized calcium, inorganic phosphorus, alkaline phosphatase, magnesium, total vitamin D and urinary calcium-to-creatinine ratio. SPSS 24 was used for data analysis. RESULTS: Of the 384 subjects, 248(65%) were male and 136(35%) were female. Overall mean age was 48±19years. Of the total, 302(786%) had parathyroid issues, with 244(81%) having secondary hyperparathyroidism. Mean serum total calcium, phosphorus, ionized calcium, magnesium and total vitamin D were 8.98±1.52 mg/dl, 4.0±1.30 mg/dl, 4.65±0.52 mg/dl, 2.11±0.27 mg/dl and 20.5±8.52 ngml respectively. Of the patients diagnosed with secondary hyperparathyroidism, 72.2% patients had chronic kidney disease and 20.2% had isolated vitamin D deficiency. CONCLUSIONS: Parathyroid disorders had significant impact on bone health. Moreover, secondary hyperparathyroidism was seen to be emerging as a major endocrine problem, especially in chronic kidney disease patients and vitamin D-deficient individuals.

Three Mutations in the Bilateral Frontoparietal Polymicrogyria Gene GPR56 in Pakistani Intellectual Disability Families.

Bilateral frontoparietal polymicrogyria (BFPP, MIM 606854) is a heterogeneous autosomal recessive disorder of abnormal cortical lamination, leading to moderate-to-severe intellectual disability (ID), seizure disorder, and motor difficulties, and caused by mutations in the G protein-coupled receptor 56 ( GPR56 ) gene. Twenty-eight mutations in 40 different families have been reported in the literature. The clinical and neuroimaging phenotype is consistent in these cases. The BFPP cortex consists of numerous small gyral cells, with scalloping of the cortical-white matter junction. There are also associated white matter, brain stem, and cerebellar changes. GPR56 is a member of an adhesion G protein-coupled receptor family with a very long N-terminal stalk and seven transmembrane domains. In this study, we identified three families from Pakistan, ascertained primarily for ID, with overlapping approximately 1 Mb region (chr16:56,973,335-57,942,866) of homozygosity by descent, including 24 RefSeq genes. We found three GPR56 homozygous mutations, using next-generation sequencing. These mutations include a substitutional variant, c.1460T > C; p.L487P, (chr16:57693480 T > C), a 13-bp insertion causing the frameshift and truncating mutation, p.Leu269Hisfs*21 (NM_005682.6:c.803_804insCCATGGAGGTGCT; Chr16: 57689345_57689346insCCATGGAGGTGCT), and a truncating mutation c.1426C > T; p.Arg476* (Chr16:57693446C > T). These mutations fully segregated with ID in these families and were absent in the Exome Aggregation Consortium database that has approximately 8,000 control samples of South Asian origin. Two of these mutations have been reported in ClinVar database, and the third one has not been reported before. Three families from Pakistan with GPR56 mutations have been reported before. With the addition of our findings, the total number of mutations reported in Pakistani patients now is six. These results increase our knowledge regarding the mutational spectrum of the GPR56 gene causing BFPP/ID.

Bystander signaling via oxidative metabolism.

The radiation-induced bystander effect (RIBE) is the initiation of biological end points in cells (bystander cells) that are not directly traversed by an incident-radiation track, but are in close proximity to cells that are receiving the radiation. RIBE has been indicted of causing DNA damage via oxidative stress, besides causing direct damage, inducing tumorigenesis, producing micronuclei, and causing apoptosis. RIBE is regulated by signaling proteins that are either endogenous or secreted by cells as a means of communication between cells, and can activate intracellular or intercellular oxidative metabolism that can further trigger signaling pathways of inflammation. Bystander signals can pass through gap junctions in attached cell lines, while the suspended cell lines transmit these signals via hormones and soluble proteins. This review provides the background information on how reactive oxygen species (ROS) act as bystander signals. Although ROS have a very short half-life and have a nanometer-scale sphere of influence, the wide variety of ROS produced via various sources can exert a cumulative effect, not only in forming DNA adducts but also setting up signaling pathways of inflammation, apoptosis, cell-cycle arrest, aging, and even tumorigenesis. This review outlines the sources of the bystander effect linked to ROS in a cell, and provides methods of investigation for researchers who would like to pursue this field of science.