BACKGROUND AND OBJECTIVE

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the causative agent of COVID-19 has significantly challenged the public health landscape in late 2019. After almost 3 years of the first ever SARS-CoV-2 case, the World Health Organization (WHO) declared the end of this global health emergency in May 2023. Although, despite the subsequent drop of COVID-19 cases, the SARS-CoV-2 infection still exhibited multiple waves of infection, primarily attributed to the appearance of new variants. Five of these variants have been classified as Variants of Concern (VOC): Alpha, Beta, Gamma, Delta, and the most recent, Omicron. Therefore, the development of methods for the timely and accurate detection of viral variants remains fundamental, ensuring an ongoing and effective response to the disease. This study aims to evaluate the feasibility of the application of an in-house approach in genomic surveillance for the detection of SARS-CoV-2 variants using in silico designed primers.

The primers used for the study were particularly designed based on conserved regions of certain genes in the virus, targeting distinct mutations found in known variants of SARS-CoV-2. Viral RNA extracts from nasopharyngeal samples (n=14) were subjected to quantitative and qualitative tests (Nanodrop and AGE). Selected samples were then analyzed by RT-PCR and amplicons were submitted for sequencing. Sequence alignment analysis was carried out to identify the prevailing COVID-19 variant present in the sample population.

The study findings demonstrated that the in-house method was able to successfully amplify conserved sequences (spike, envelope, membrane, ORF1ab) and enabled identification of the circulating SARS-CoV-2 variant among the samples. Majority of the samples were identified as Omicron variant. Three out of four designed primers effectively bound into the conserved sequence of target genes present in the sample, revealing the specific SARSCoV-2 variant. The detected mutations characterized for Omicron found in the identified lineages included K417N, S477N, and P681H which were also identified as mutations of interest. Furthermore, identification of the B.1.448 lineage which was not classified in any known variant also provided the potential of the developed in-house method in detecting unknown variants of COVID-19.

Among the five VOCs, Omicron is the most prevalent and dominant variant. The in-house direct PCR product sequencing surveillance (DPPSS) method provided an alternative platform for SAR-CoV-2 variant analysis which is accessible and affordable than the conventional diagnostic surveillance methods and the whole genome sequencing. Further evaluation and improvements on the oligonucleotide primers may offer significant contribution to the development of a specific and direct PCRbased detection of new emerging COVID-19 variants.

BACKGROUND AND OBJECTIVES

Cell lines serve as invaluable tools in studying lung cancer biology and developing new therapies to combat the disease. However, commercially available cell lines are typically of Caucasian origin and may be less representative of the local genetic background. To address this, our lab previously immortalized cells from pleural fluid of a Filipino non-small cell lung cancer (NSCLC) patient via CDK4 transduction. Copy number variations (CNVs) are a type of genetic variation which may affect physiology and disease by disrupting gene function or altering gene expression, and in cancer, these may be associated with patient outcomes. CNV profiling can be valuable for understanding the biology of our immortalized cells and identifying genes that could serve as potential targets for diagnostic, prognostic, and therapeutic interventions. This study aimed to characterize previously immortalized NSCLC-derived cells, GL01, in comparison with an established lung adenocarcinoma (LUAD) cell line, A549, through whole-genome microarray-based copy number profiling.

DNA was extracted from GL01 and A549 cells using a commercially-available silica-based DNA extraction kit. DNA extracts were quantified and normalized for microarray analysis. Whole-genome copy number profiling was done using the OncoScan CNV Plus Assay following the manufacturer’s protocols, and data was analyzed using the Chromosome Analysis Suite software. Functional analysis of genes identified to be involved in copy number aberrations was done using the PANTHER Classification System.

Copy number aberrations span 1,592,737,105 bp in GL01 and 1,715,708,552 bp in A549, with a high degree of concordance between the two. Large-scale and focal copy number aberrations previously identified to be recurrent in various LUAD cohorts were present in both GL01 and A549. Focal copy number aberrations associated with previously described lung cancer-related genes involve the PDE4D gene in GL01 and the SKIL and CDKN2A/CDKN2B genes in both GL01 and A549. PANTHER Pathway analysis of genes positively correlated with mRNA expression showed that the ubiquitin proteasome pathway was significantly overrepresented in both GL01 (FDR p = 0.000074) and A549 (FDR p = 0.000075), with 20 genes involved. Additionally, the KRAS:p.G12C/S:c.34G>T/A somatic mutation variant was detected in both GL01 and A549.

This study provides a method for identifying potentially clinically-relevant genes associated with a sample’s copy number aberrations and the pathways they represent, providing personalized mechanistic, prognostic, and therapeutic insights into the cancer biology of our cells.

Background and Objectives: Cell lines serve as invaluable tools in studying lung cancer biology and developing new therapies to combat the disease. However, commercially available cell lines are typically of Caucasian origin and may be less representative of the local genetic background. To address this, our lab previously immortalized cells from pleural fluid of a Filipino non-small cell lung cancer (NSCLC) patient via CDK4 transduction. Copy number variations (CNVs) are a type of genetic variation which may affect physiology and disease by disrupting gene function or altering gene expression, and in cancer, these may be associated with patient outcomes. CNV profiling can be valuable for understanding the biology of our immortalized cells and identifying genes that could serve as potential targets for diagnostic, prognostic, and therapeutic interventions. This study aimed to characterize previously immortalized NSCLC-derived cells, GL01, in comparison with an established lung adenocarcinoma (LUAD) cell line, A549, through whole-genome microarray-based copy number profiling. Methods: DNA was extracted from GL01 and A549 cells using a commercially-available silica-based DNA extraction kit. DNA extracts were quantified and normalized for microarray analysis. Whole-genome copy number profiling was done using the OncoScan CNV Plus Assay following the manufacturer’s protocols, and data was analyzed using the Chromosome Analysis Suite software. Functional analysis of genes identified to be involved in copy number aberrations was done using the PANTHER Classification System. Results: Copy number aberrations span 1,592,737,105 bp in GL01 and 1,715,708,552 bp in A549, with a high degree of concordance between the two. Largescale and focal copy number aberrations previously identified to be recurrent in various LUAD cohorts were present in both GL01 and A549. Focal copy number aberrations associated with previously described lung cancer-related genes involve the PDE4D gene in GL01 and the SKIL and CDKN2A/CDKN2B genes in both GL01 and A549. PANTHER Pathway analysis of genes positively correlated with mRNA expression showed that the ubiquitin proteasome pathway was significantly overrepresented in both GL01 (FDR p = 0.000074) and A549 (FDR p = 0.000075), with 20 genes involved. Additionally, the KRAS:p.G12C/S:c.34G>T/A somatic mutation variant was detected in both GL01 and A549. Conclusion This study provides a method for identifying potentially clinically-relevant genes associated with a sample’s copy number aberrations and the pathways they represent, providing personalized mechanistic, prognostic, and therapeutic insights into the cancer biology of our cells.
carcinoma, non-small cell lung ; adenocarcinoma of lung

Background: Management of COVID--19 patients during surges have been a challenge as hospitals have to deal with staff, room, and medication shortages. Among these medications is tocilizumab which is given to patients with severe/critical conditions. In Ospital ng Makati, patients are given baricitinib as alternative immunomodulator to prevent possible cytokine storm during tocilizumab shortages. The current recommendation for baricitinib is to give it in addition to dexamethasone and remdesivir for hospitalized COVID-19 patients requiring low to high-flow oxygen, and non-invasive ventilation. However, there is not enough evidence to recommend it as an alternative to tocilizumab in COVID--19 patients. This study aims to find out the real-world efficacy of baricitinib in addition to standard of care among admitted patients with severe COVID-19 pneumonia admitted in Ospital ng Makati. Methods: This is a retrospective, case control study that reviewed records of adult patients admitted at Ospital ng Makati from December 2020 to May 2021 due to severe COVID-19. Patients who were given standard of care was compared to those who were given baricitinib by measuring the duration of clinical improvement, in-hospital all-cause mortality, number of hospital stay, and progression to acute respiratory distress syndrome (ARDS) and need for mechanical ventilator. Results: The use of baricitinib led to a faster improvement time (10 vs 12 days) however did not reach level of significance (p=0.069). There was also no significant difference in the mortality, number of hospital days, and progression to ARDS between the two groups. Conclusion There is not enough evidence to recommend baricitinib as an alternative to tocilizumab in patients with severe COVID--19 infection.
COVID-19 ; Standard of Care

Background: and Purpose Recent studies suggested an increased incidence of cerebral venous thrombosis (CVT) during the coronavirus disease 2019 (COVID-19) pandemic. We evaluated the volume of CVT hospitalization and in-hospital mortality during the 1st year of the COVID-19 pandemic compared to the preceding year. Methods: We conducted a cross-sectional retrospective study of 171 stroke centers from 49 countries. We recorded COVID-19 admission volumes, CVT hospitalization, and CVT in-hospital mortality from January 1, 2019, to May 31, 2021. CVT diagnoses were identified by International Classification of Disease-10 (ICD-10) codes or stroke databases. We additionally sought to compare the same metrics in the first 5 months of 2021 compared to the corresponding months in 2019 and 2020 (ClinicalTrials.gov Identifier: NCT04934020). Results: There were 2,313 CVT admissions across the 1-year pre-pandemic (2019) and pandemic year (2020); no differences in CVT volume or CVT mortality were observed. During the first 5 months of 2021, there was an increase in CVT volumes compared to 2019 (27.5%; 95% confidence interval [CI], 24.2 to 32.0; P<0.0001) and 2020 (41.4%; 95% CI, 37.0 to 46.0; P<0.0001). A COVID-19 diagnosis was present in 7.6% (132/1,738) of CVT hospitalizations. CVT was present in 0.04% (103/292,080) of COVID-19 hospitalizations. During the first pandemic year, CVT mortality was higher in patients who were COVID positive compared to COVID negative patients (8/53 [15.0%] vs. 41/910 [4.5%], P=0.004). There was an increase in CVT mortality during the first 5 months of pandemic years 2020 and 2021 compared to the first 5 months of the pre-pandemic year 2019 (2019 vs. 2020: 2.26% vs. 4.74%, P=0.05; 2019 vs. 2021: 2.26% vs. 4.99%, P=0.03). In the first 5 months of 2021, there were 26 cases of vaccine-induced immune thrombotic thrombocytopenia (VITT), resulting in six deaths. Conclusions During the 1st year of the COVID-19 pandemic, CVT hospitalization volume and CVT in-hospital mortality did not change compared to the prior year. COVID-19 diagnosis was associated with higher CVT in-hospital mortality. During the first 5 months of 2021, there was an increase in CVT hospitalization volume and increase in CVT-related mortality, partially attributable to VITT.

INTRODUCTION: Salba-chia (Salvia hispanica L.) is a popular functional food containing high levels of protein, total dietary fiber, and is an excellent source of α-linolenic acid. Chia seeds significantly decreases weight, suppresses appetite, and has a potential benefit in the management of Type 2 diabetes mellitus (T2DM). This study aimed to determine the effectiveness of chia seeds as an adjuvant treatment for T2DM. METHODS: Randomized controlled trials from 1990 onwards involving Type 2 diabetic patients given chia seed were included. PubMed, Cochrane, ClinicalKey, Google Scholar, and Hinari were searched systematically using MeSH terms “chia”, “Salvia hispanica”, “dietary supplement”, and “diabetes”. The quality of trials was assessed using the Cochrane Collaboration tool. Data on the study design, blinding status, characteristics of participants, medications taken by participants, chia seed intervention, comparator, duration of intake, and interval of assessment were extracted. The percent change of outcome from baseline was compared between the chia and control groups. RESULTS: Four randomized trials with a total of 213 diabetic patients were enrolled in the treatment group using ground salba-chia or the control group using bran. The supplementation of chia resulted in a statistically significant decrease in fasting glucose (-2.90 mmol/L; 95% CI, -3.08, -2.72; p < 0.001), waist circumference (-2.49 cm; 95% CI -2.81, -2.17; p < 0.001), total cholesterol (-2.72 mmol/L; 95% CI -3.68, -1.74; p < 0.001), HDL (-3.69 mmol/L; 95% CI -3.95, -3.42; p < 0.001), LDL (-3.22 mmol/L; 95% CI -4.08, -2.36; p < 0.001); and an increase adiponectin levels (6.50 mg/L; 95% CI 6.25, 6.25; p < 0.001). CONCLUSION Intake of chia seeds resulted in a statistically significant decrease in fasting blood glucose, waist circumference, total cholesterol levels, HDL and LDL cholesterol levels, and increased adiponectin. Chia seeds are generally safer and have lesser side effects compared to the placebo. Chia is effective as adjunctive treatment for Type 2 diabetic patients.

Objectives: The objective of this evaluation was to assess the effectiveness of Mindfulness for Safe Schools, a mindfulness-based intervention adapted for sexual abuse prevention during peer-to-peer dating among Filipino public school children in Grades 7 and 8. It was hoped that through the intervention, children would be able to regulate their emotions so that they do not react impulsively to emotionally stimulating events, especially during peer dating. The study consists of four levels of evaluation: reaction, learnings, and behaviors of teachers toward the program, as well as effect of the intervention on emotion regulation and peer conformity among students. Methods: This study utilized a mixed methods design using a concurrent embedded method. For teachers, quantitative surveys and focused group discussions were conducted to determine their reactions to the training, their learnings, and behaviors after the program, as well as their observations of students’ responses to the intervention. Focused group discussions were analyzed through thematic analysis. Effect of the program on emotion regulation and peer conformity among students were determined mainly through a pre and post-test survey and analyzed through paired samples t-test. Video content analysis of the classroom delivery was also conducted to determine student engagement during the program. Results: Teachers reacted favorably to the training workshops and were able to use what they learned from the workshops to increase their patience and understanding towards themselves, their job, and their students. Students also reacted favorably to the Mindfulness for Safe Schools modules and were observed to use the skills taught in the modules to regulate their emotions. Emotion regulation improved (t=3.47, significant with p=0.00) and susceptibility to peer pressure decreased (t=8.94, significant with p=0.00) for Grade 8 students (n=950) after the modules were delivered. However, teachers reported implementation issues, such as conflicting requirements of the program with their official workload, which may have affected program effects. Conclusion Our findings indicate that Mindfulness for Safe Schools was associated with improvements in emotional awareness, management of negative emotions, and showing care and respect for student peers. It also suggests that integrating mindfulness interventions in schools requires close coordination with all stakeholders: teachers, schools, and appropriate government divisions to ensure fidelity and reaching desired effects.
Mindfulness