Hub genes identification and association of key pathways with hypoxia in cancer cells: A bioinformatics analysis.

Three human cancer cell lines (A549, HCT116, and HeLa) were used to investigate the molecular mechanisms and potential prognostic biomarkers associated with hypoxia. We obtained gene expression data from Gene Expression Omnibus (GEO) datasets GSE11704, GSE147384, and GSE38061, which included 5 hypoxic and 8 control samples. Using the GEO2R tool and Venn diagram software, we identified common differentially expressed genes (cDEGs). The cDEGs were then subjected to Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis by employing DAVID. The hub genes were identified from critical PPI subnetworks through CytoHuba plugin and these genes' prognostic significance and expression were verified using Kaplan-Meier analysis and Gene Expression Profiling Interactive Analysis (GEPIA), respectively. The research showed 676 common DEGs (cDEGs), with 207 upregulated and 469 downregulated genes. The STRING analysis showed 673 nodes and 1446 edges in the PPI network. We identified 4 significant modules and 19 downregulated hub genes. GO analysis revealed all of them were majorly involved in ribosomal large subunit assembly and biogenesis, rRNA processing, ribosome biogenesis, translation, RNA & protein binding frequently at the sites of nucleolus and nucleoplasm while 11 were significantly associated with a better prognosis of hypoxic tumors. Our research sheds light on the molecular mechanisms that underpin hypoxia in human cancer cell lines and identifies potential prognostic biomarkers for hypoxic tumors.

Population-level median cycle threshold (Ct) values for asymptomatic COVID-19 cases can predict the trajectory of future cases.

BACKGROUND: Recent studies indicate that the population-level SARS-CoV-2 cycle threshold (Ct) values can inform the trajectory of the pandemic. The presented study investigates the potential of Ct values in predicting the future of COVID-19 cases. We also determined whether the presence of symptoms could change the correlation between Ct values and future cases. METHODS: We examined the individuals (n = 8660) that consulted different sample collection points of a private diagnostic center in Pakistan for COVID-19 testing between June 2020 and December 2021. The medical assistant collected clinical and demographic information. The nasopharyngeal swab specimens were taken from the study participants and real-time reverse transcriptase polymerase chain reaction (RT-PCR) was used to detect SARS-CoV-2 in these samples. RESULTS: We observed that median Ct values display significant temporal variations, which show an inverse relationship with future cases. The monthly overall median Ct values negatively correlated with the number of cases occurring one month after specimen collection (r = -0.588, p <0.05). When separately analyzed, Ct values for symptomatic cases displayed a weak negative correlation (r = -0.167, p<0.05), while Ct values from asymptomatic cases displayed a stronger negative correlation (r = -0.598, p<0.05) with the number of cases in the subsequent months. Predictive modeling using these Ct values closely forecasted the increase or decrease in the number of cases of the subsequent month. CONCLUSIONS: Decreasing population-level median Ct values for asymptomatic COVID-19 cases appear to be a leading indicator for predicting future COVID-19 cases.

Dyslipidemia and impaired liver function biomarkers in patients with hepatitis B liver cirrhosis.

Objective: This study was conducted to determine changes in lipid metabolism and liver enzyme status among HBV-positive patients with liver cirrhosis. Methods: A total of 300 HBV-positive patients with liver cirrhosis and 200 healthy controls were included in this case-control study. The patients were recruited from several tertiary care hospitals in Lahore from March to October 2021. Their blood samples were collected and analyzed for HBsAg, HBeAg, liver function biomarkers, and serum lipids. Liver cirrhosis was confirmed by ultrasonography and liver biopsy. The data were analyzed with chi-square test, Student's t-test, logistic regression, and ROC curve analysis. Results: Serum liver function biomarkers were significantly higher, and serum lipid levels were substantially lower, in HBV-infected patients with liver cirrhosis than in controls. No significant associations of sex and age with dyslipidemia were observed in patients with cirrhosis. Grading and staging scores for liver cirrhosis were negatively associated with total cholesterol levels. Moreover, sex and high levels of liver enzymes were significant risk factors associated with dyslipidemia in HBV-positive patients with liver cirrhosis. The optimum cut-off values of liver enzymes and serum lipids for the prognosis of liver cirrhosis exceeded normal ranges. Conclusion: Serum lipid concentrations may serve as a clinical index to assess liver damage in HBV-positive patients.

Cancer Awareness Measure (CAM) and Cancer Awareness Measure MYthical Causes Scale (CAM-MY) scores in Pakistani population.

Lifestyle modifications could prevent almost one-third to one-half of all cancer cases. The awareness of cancer risk factors could motivate people to make such changes in their behaviors and lifestyles. This work aims to investigate the cancer awareness level in the Pakistani population. Telephone interviews of 657 individuals in Pakistan were carried out using the Cancer Awareness Measure (CAM) and Cancer Awareness Measure-MYthical Causes Scale (CAM-MY). We observed that participants scored significantly better on the CAM scale than the CAM-MY scale, and CAM scores were negatively associated with CAM-MY scores. Years of formal education or a biology major at undergraduate or graduate level did not affect our population's cancer awareness levels. Age displayed a weak but statistically significant negative association with CAM scores. Most participants failed to identify modifiable cancer risk factors, e.g., low physical activity. Efforts should be made to improve awareness of modifiable risk factors. We observed that brief training sessions could markedly improve people's understanding of cancer risk factors and myths.

Factors associated with cycle threshold values (Ct-values) of SARS-CoV2-rRT-PCR.

BACKGROUND: Presented work studies the association of COVID-19 severity, patient demographics, and clinical history with cycle threshold (Ct) values of SARS CoV2-rRT-PCR. We studied the Ct values for Orf1ab, N, and RdRp genes in association with all the factors mentioned above. METHODS AND RESULTS: We examined the individuals (n = 6331) that consulted two private diagnostic centers for COVID-19 testing. SARS-CoV-2 was detected by RT-PCR assays using different commercial kits. Clinical and demographic information was collected by the attending health care professional. Ct values were not associated with the age, sex, or clinical history of the patient. Orf1ab and N genes Ct values were only weakly associated with symptoms at the time of the SARS-CoV-2 RT-PCR test. Also, the distributions of Ct values in SARS-CoV-2 positive patients are very similar irrespective of symptomatology. CONCLUSION: We conclude that the Ct values may have limitations in reliably predicting COVID-19 severity and should be used or reported with caution.

COVID-19 severity: Studying the clinical and demographic risk factors for adverse outcomes.

BACKGROUND: The primary goal of the presented cross-sectional observational study was to determine the clinical and demographic risk factors for adverse coronavirus disease 2019 (COVID-19) outcomes in the Pakistani population. METHODS: We examined the individuals (n = 6331) that consulted two private diagnostic centers in Lahore, Pakistan, for COVID-19 testing between May 1, 2020, and November 30, 2020. The attending nurse collected clinical and demographic information. A confirmed case of COVID-19 was defined as having a positive result through real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay of nasopharyngeal swab specimens. RESULTS: RT-PCR testing was positive in 1094 cases. Out of which, 5.2% had severe, and 20.8% had mild symptoms. We observed a strong association of COVID-19 severity with the number and type of comorbidities. The severity of the disease intensified as the number of comorbidities increased. The most vulnerable groups for the poor outcome are patients with diabetes and hypertension. Increasing age was also associated with PCR positivity and the severity of the disease. CONCLUSIONS: Most cases of COVID-19 included in this study developed mild symptoms or were asymptomatic. Risk factors for adverse outcomes included older age and the simultaneous presence of comorbidities.

Expression of lipid transport-associated genes in lipid-deprived cancer cells.

Cancer cells are known to significantly alter their lipid profiles in response to changes in extracellular lipid availability. Recent studies have shown that in response to lipid deprivation, cancer cells display significant changes in their cellular lipid homeostasis. These changes have been linked to the modulation of de novo lipid synthesis pathways that are markedly altered under lipid-deprived growth conditions. However, the effects of such environment on intracellular lipid trafficking-that could also affect cellular lipid homeostasis-have not been widely investigated. The presented work studies the effect of lipid deprivation on expression of genes for lipid transport proteins (LTPs) in cancer cell lines.