Network Pharmacology and Experimental Validation to Explore the Potential Mechanism of Nigella sativa for the Treatment of Breast Cancer.

Breast cancer is a prevalent and potentially life-threatening disease that affects women worldwide. Natural products have gained attention as potential anticancer agents due to their fewer side effects, low toxicity, and cost effectiveness compared to traditional chemotherapy drugs. In the current study, the network pharmacology approach was used following a molecular docking study to evaluate the therapeutic potential of N. sativa-derived phytochemicals against breast cancer. Specifically, the study aimed to identify potential anticancer agents targeting key proteins implicated in breast cancer progression. Five proteins (i.e., EGFR, MAPK3, ESR1, MAPK1, and PTGS2) associated with breast cancer were selected as receptor proteins. Fourteen phytochemicals from N. sativa were prioritized based on drug-likeness (DL) and oral bioavailability (OB) parameters (with criteria set at DL > 0.18 and OB > 30%, respectively). Subsequent analysis of gene targets identified 283 overlapping genes primarily related to breast cancer pathogenesis. Ten hub genes were identified through topological analysis based on their significance in the KEGG pathway and GO annotations. Molecular docking revealed strong binding affinities between folic acid, betulinic acid, stigmasterol, and selected receptor proteins. These phytochemicals also demonstrated druggability potential. In vitro experiments in the MDA-MB-231 breast cancer cell line revealed that betulinic acid and stigmasterol significantly reduced cell viability after 24 h of treatment, confirming their anticancer activity. Furthermore, in vivo evaluation using a DMBA-induced rat model showed that betulinic acid and stigmasterol contributed to the significant recovery of cancer markers. This study aimed to explore the mechanisms underlying the anticancer potential of N. sativa phytochemicals against breast cancer, with the ultimate goal of identifying novel therapeutic candidates for future drug development. Overall, these results highlight betulinic acid and stigmasterol as promising candidates to develop novel anticancer agents against breast cancer. The comprehensive approach of this study, which integrates network pharmacology and molecular docking study and its experimental validation, strengthens the evidence supporting the therapeutic benefits of N. sativa-derived phytochemicals in breast cancer treatment, making them promising candidates for the development of novel anticancer agents against breast cancer.

Exploring the Potential of Plant Bioactive Compounds against Male Infertility: An In Silico and In Vivo Study.

Infertility is a well-recognized multifactorial problem affecting the majority of people who struggle with infertility issues. In recent times, among infertility cases, the male factor has acquired importance, and now it contributes to approximately half of the infertility cases because of different abnormalities. In the current study, we used natural phytochemicals as potential drug-lead compounds to target different receptor proteins that are involved in the onset of male infertility. A set of 210 plant phytochemicals were docked counter to active site residues of sex hormone-binding globulin, a disintegrin and metalloproteinase 17, and DNase I as receptor proteins. On the basis of binding scores and molecular dynamics simulation, the phytochemicals tricin, quercetin, malvidin, rhamnetin, isorhamnetin, gallic acid, kaempferol, esculin, robinetin, and okanin were found to be the potential drug candidates to treat male infertility. Molecular dynamics simulation showed tricin as a strong inhibitor of all selected receptor proteins because the ligand-protein complexes remained stabilized during the entire simulation time of 100 ns. Further, an in vivo study was designed to evaluate the effect of tricin in male rats with nicotine-induced infertility. It was explored that a high dose of tricin significantly reduced the levels of alanine transaminase, aspartate transaminase, urea, creatinine, cholesterol, triglyceride, and low-density lipoprotein and raised the level of high-density lipoprotein in intoxicated male rats. A high dose of tricin also increased the reproductive hormones (i.e., testosterone, luteinizing hormone, follicle-stimulating hormone, and prolactin) and reduced the level of DHEA-SO4. The phytochemical (tricin, 10 mg/kg body weight) also showed significant improvement in the histo-architecture after nicotine intoxication in rats. From the current study, it is concluded that the phytochemical tricin could serve as a potential drug candidate to cure male infertility.

Underlying Mechanisms of Bergenia spp. to Treat Hepatocellular Carcinoma Using an Integrated Network Pharmacology and Molecular Docking Approach.

Hepatocellular carcinoma (HCC) is the fifth most common and fatal cancer reported, representing 72.5% of malignancies around the world. The majority of HCC incidents have been associated with infections caused by hepatitis B and C viruses. Many first- and second-line conventional drugs, e.g., sorafenib, cabozantinib, or ramucirumab, have been used for the management of HCC. Despite different combinational therapies, there are still no defined biomarkers for an early stage diagnosis of HCC. The current study evaluated the potential of Bergenia stracheyi, Bergenia ciliata, Bergenia pacumbis, and Bergenia purpurascens, which belong to the family Saxifragaceae, to treat HCC using an integrated network pharmacology and molecular docking approach. Four active phytochemicals were selected based on oral bioavailability (OB) and drug likeness (DL) parameters. The criteria of phytochemical selection were set to OB > 30% and DL > 0.18. Similarly, the gene targets related to Bergenia spp. and the genes related to HCC were retrieved from different databases. The integration of these genes revealed 98 most common overlapping genes, which were mainly interrelated with HCC pathogenesis. Ultimately, the 98 Bergenia-HCC associated genes were used for protein-protein interaction (PPI), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and Gene Ontology (GO) enrichment analyses. Finally, the topological analysis revealed the top ten hub genes with maximum degree rank. From the top ten genes, STAT3, MAPK3, and SRC were selected due to their involvement in GO annotation and KEGG pathway. To confirm the network pharmacology results, molecular docking analysis was performed to target STAT3, MAPK3, and SRC receptor proteins. The phytochemical (+)-catechin 3-gallate exhibited a maximum binding score and strong residue interactions with the active amino acids of MAPK3-binding pockets (S-score: -10.2 kcal/mol), SRC (S-score: -8.9 kcal/mol), and STAT3 (S-score: -8.9 kcal/mol) as receptor proteins. (+)-Catechin 3-gallate and ß-sitosterol induced a significant reduction in cell viability in HepG2 after 24 h of treatment in a dose-dependent manner. The results of this study explore the potential of (+)-catechin 3-gallate and ß-sitosterol, which can be used in the future as potential drug candidates to suppress HCC.

Evaluation of the clinical, biochemical, and genetic presentation of neonatal and adult-onset 5,10-methylene tetrahydrofolate reductase (MTHFR) deficiency in patients from Pakistan.

OBJECTIVES: To study the biochemical, clinical and molecular characteristics of 5,10- methylenetetrahydrofolate reductase (MTHFR) deficiency in Pakistani patients from a single center. METHODS: Medical charts, urine organic acid chromatograms, plasma methionine and Hcys levels, and molecular testing results of MTHFR gene of patients presenting at the Biochemical Genetics Clinic, AKUH from 2016 to 2022 were reviewed. RESULTS: Neonatal MTHFR deficiency was found in five patients. The median (IQR) age of symptom onset and diagnosis were 18 (8.5-22) and 26 (16.5-31) days. The median lag between symptom onset and diagnosis was 8 (4.5-12.5) days. The median age of treatment initiation and duration of treatment were 26 (16.5-49) and 32 (25.5-54) days. The most common clinical features were lethargy, poor feeding, and seizures. The MTHFR gene sequencing revealed homozygous variants p.K510K, p.R567*, and p.R157W. Renal insufficiency manifesting as elevated serum creatinine and responding to betaine therapy was noted in one patient. This has not been previously reported in neonatal MTHFR deficiency and may reflect engagement of alternate pathways of remethylation. Adult onset MTHFR deficiency was found in six patients, with a heterogeneous neurological presentation. The median lag between symptoms onset and diagnosis was 7 (3-11) years. MTHFR gene sequencing revealed homozygous variant p.A195V in five patients from one family and p.G261V in the other. Two of the five reported variants are novel that include p.R157W and p.G261V. CONCLUSIONS: Eleven patients of this rare disorder from a single center indicate the need for clinical awareness and appropriate biochemical evaluation to ensure optimal outcomes.

Interleukin-6 (IL-6) as a Predictor of Clinical Outcomes in Patients with COVID-19.

BACKGROUND: Interleukin-6 (IL-6) has been known to be involved in immune regulation, inflammatory response, and metabolism. It is also recognized as the major cause to underscore the pathology of severe COVID-19 patients. However, it remains to be seen if IL-6 is superior to other inflammatory biomarkers in ascertaining clinical severity and mortality rate for COVID-19. This study aimed to determine the value of IL-6 as a predictor of severity and mortality in COVID-19 patients and compare it with other pro-inflammatory biomarkers in the South Asian region. METHODS: An observational study was conducted, including all adult SARS-CoV-2 patients who had undergone IL-6 testing from December 2020 to June 2021. The patients' medical records were reviewed to collect demographic, clinical, and biochemical data. Other pro-inflammatory biomarkers apart from IL-6 included Neutrophils to Lymphocyte Ratio (NLR), D-dimer, C-reactive protein (CRP), ferritin, lactate dehydrogenase (LDH), and procal-citonin for analysis. SPSS version 22.0 was utilized. RESULTS: Out of the 393 patients who underwent IL-6 testing, 203 were included in the final analysis with a mean (SD) age of 61.9 years (12.9) and 70.9% (n = 144) were male. Fifty-six percent (n = 115) subjects had critical disease. IL-6 levels were elevated (> 7 pg/mL) in 160 (78.8%) patients. Levels of IL-6 significantly correlated with age, NLR, D-dimer, CRP, ferritin, LDH, length of stay, clinical severity, and mortality. All the inflammatory markers were significantly increased in critically ill and expired patients (p < 0.05). The receiver operator curve showed that IL-6 had the best area under the curve (0.898) compared to other pro-inflammatory biomarkers for mortality with comparable results for clinical severity. CONCLUSIONS: Study findings show that though IL-6 is an effective marker of inflammation and can be helpful for clinicians in recognizing patients with severe COVID-19. However, we still need further studies with larger sample size.

L-2-hydroxyglutaric aciduria - review of literature and case series.

L-2-hydroxyglutaric aciduria (L2HGA) is an autosomal recessive, slowly progressive neurodegenerative disease characterized by psychomotor delay and cerebellar dysfunction. The biochemical hallmark is increased concentrations of L2HG in body fluids. Brain MRI exhibits characteristic centripetal extension of the white matter involvement that differentiates it from other leukodystrophies. The authors report two sisters from Pakistan with L2HGA with 4 years of follow-up. The authors have also compared the clinical outcome of our patients with 45 previously reported patients with L2HGA for whom treatment and clinical outcome was reported. Case presentation: The authors report two sisters with L2HGA from Pakistan born to consanguineous parents. The 15- and 17-year-old girls presented with psychomotor delay, seizures, ataxia, intentional tremors, and dysarthria. Both had normal anthropometric measurements for age. Exaggerated tendon reflexes and bilateral sustained ankle clonus were observed in addition to cerebellar signs. Urine organic acids analysis showed marked excretion of 2-hydroxyglutaric acid, chiral differentiation of 2-hydroxyglutaric acid showed it to be L2HGA. Brain MRI of the 15-year-old showed diffuse subcortical white matter changes evident by T2/FLAIR hyperintense signals bilaterally, particularly in the frontal region in the centripetal distribution with some diffusion restriction along involvement of globus pallidus. The characteristic MRI pattern raised the suspicion of L2HGA. Targeted L2HGDH sequencing identified a homozygous pathogenic variant, c.829C>T (p.Arg227*) in L2HGDH gene in both girls. Both parents were heterozygous carriers of the familial variant. Conclusion: Neuroradiological features of centripetal subcortical leukoencephalopathy with basal ganglia and dentate nuclei involvement are rather specific to L2HGA and should lead to further biochemical investigations to look for L2HGA and L2HGDH gene sequencing.

Characterization and anticancer potential of Withania somnifera fruit bioactives (a native species to Pakistan) using gas chromatography-mass spectrometer, nuclear magnetic resonance and liquid chromatography-mass spectrometry-electrospray ionization.

INTRODUCTION: Withania somnifera (W. somnifera) is a plant with remarkable pharmacological properties. The plant has an impressive profile of medicinal uses in the folk medicine system of several civilizations. AIM: This comprehensive study is aimed to characterize phytochemicals in fruit of W. somnifera and tested for anticancer potential to find out active candidate in disease prevention and treatment. METHODS: The bioactive components from W. somn-ifera fruit were extracted with polar and non-polar solvents. Anticancer potential of the isolated bioactive was assessed against different cancer cell lines through MTT assay and Incucytes imaging analysis. The extracts were characterized for secondary metabolites using GC-MS (gas chromatography-mass spectrometer), LCMS (liquid chromatography-mass spectrometry)-ESI (electrospray Ionization) and 1H-NMR (electrospray Ionization) techniques. RESULTS: Both freeze-dried and rotary evaporator con-densed extracts exhibited anticancer potential against MDA-MB-231, MCF7- SKOV3 and SKBR3 cell lines. The tested extracts have cell growth inhibition potential ag-ainst mammalian cancer cell line. Hexacosanedioic acid purified from -hexane extract through HPLC was inves-tigated for its cytotoxicity against breast cancer cell line SKBR3 by using Incucytes imaging analysis. CONCLUSION: We found that a variety of bioactive compounds existed in this plant. One identified compound that was not investigated for cytotoxicity in previous studies was purified and its application showed cytotoxicity on breast cancer cell lines. A number of bioactive identified from fruit may have an effective potential for development into chemotherapy drugs.

Utilizing augmented artificial intelligence for aminoacidopathies using collaborative laboratory integrated reporting- A cross-sectional study.

Introduction: Plasma amino acids profiling can aid in the screening and diagnosis of aminoacidopathies. The goal of the current study was to analyze and report the metabolic profiles of plasma amino acid (PAA) and additionally to compare PAA-reference intervals (RI) from Pakistan with more countries utilizing Clinical Laboratory Integrated Reports (CLIR). Methods: This was a cross sectional prospective single center study. Twenty-two amino acids were analyzed in each sample received for one year at the clinical laboratory. Data was divided into reference and case data files after interpretation by a team of pathologists and technologists. All PAA samples were analyzed using ion-exchange high-performance chromatography. The CLIR application of Amino Acid in Plasma (AAQP) was used for statistical analysis for both data sets and post-analytical interpretive tools using a single condition tool was applied. Result: The majority of 92% (n = 1913) of PAA profiles out of the total 2081 tests run were non-diagnostic; the PAA values were within the age-specific RI. The PAA median was in close comparison close to the 50th percentile of reference data available in CLIR software. Out of the total 2081 tests run, one hundred and sixty-eight had abnormal PAA levels; 27.38% were labeled as non-fasting samples, and the main aminoacidopathies identified were Phenylketonuria and Maple Syrup Urine Disorder. Conclusion: An agreement of >95% was observed between the reporting done by the pathologists and technologists' team and then after the application of CLIR. Augmented artificial intelligence using CLIR can improve the accuracy of reporting rare aminoacidopathies in a developing country like ours.

Urinary metabolomics using gas chromatography-mass spectrometry: potential biomarkers for autism spectrum disorder.

BACKGROUND: Diagnosis of autism spectrum disorder (ASD) is generally made phenotypically and the hunt for ASD-biomarkers continues. The purpose of this study was to compare urine organic acids profiles of ASD versus typically developing (TD) children to identify potential biomarkers for diagnosis and exploration of ASD etiology. METHODS: This case control study was performed in the Department of Pathology and Laboratory Medicine in collaboration with the Department of Pediatrics and Child Health, Aga Khan University, Pakistan. Midstream urine was collected in the first half of the day time before noon from the children with ASD diagnosed by a pediatric neurologist based on DSM-5 criteria and TD healthy controls from August 2019 to June 2021. The urine organic acids were analyzed by Gas Chromatography-Mass Spectrometry. To identify potential biomarkers for ASD canonical linear discriminant analysis was carried out for the organic acids, quantified in comparison to an internal standard. RESULTS: A total of 85 subjects were enrolled in the current study. The mean age of the ASD (n = 65) and TD groups (n = 20) was 4.5 ± 2.3 and 6.4 ± 2.2 years respectively with 72.3% males in the ASD group and 50% males in the TD group. Parental consanguinity was 47.7 and 30% in ASD and TD groups, respectively. The common clinical signs noted in children with ASD were developmental delay (70.8%), delayed language skills (66.2%), and inability to articulate sentences (56.9%). Discriminant analysis showed that 3-hydroxyisovalericc, homovanillic acid, adipic acid, suberic acid, and indole acetic were significantly different between ASD and TD groups. The biochemical classification results reveal that 88.2% of cases were classified correctly into ASD& TD groups based on the urine organic acid profiles. CONCLUSION: 3-hydroxy isovaleric acid, homovanillic acid, adipic acid, suberic acid, and indole acetic were good discriminators between the two groups. The discovered potential biomarkers could be valuable for future research in children with ASD.

GC-MS Metabolomics profiling and HR-APCI-MS characterization of potential anticancer compounds and antimicrobial activities of extracts from Picrorhiza kurroa roots.

The present study explores pharmacological potential and phytochemicals profiling of Picrorhiza kurroa extracts against mammalian cancer cell lines and pathogenic microbes. Bioactive extracts from roots of Picrorhiza kurroa were recovered in the methanol, 50% aqueous dichloromethane (50 : 50 v/v) and n-hexane. Antimicrobial activity of the bioactive extracts was assessed against selected strains of bacteria and pathogenic fungi. Aqueous dichloromethane extract showed highest zone of growth inhibition (39.06 ± 1.0 mm) towards Staphylococcus aureus bacteria while methanolic extract showed the lowest inhibition (6.3 ± 4.1 mm) to Escherichia coli bacteria. The tested extracts such as methanol and aqueous dichloromethane exhibited higher inhibition antifungal activity against Aspergillus flavus compared to Fusarium oxysporum. As far as cytotoxicity (MTT assay) of the tested extracts is concerned, n-hexane and aqueous dichloromethane extracts were found to be very active against all cancer cell lines (breast cancer MCF7, MDA-MB-231, SKBR3 and ovarian cancer SKOV3). A preliminary phytochemicals profiling was performed in extracts using GC-MS. Several fractions of active extract were separated with HPLC and analyzed using High Resolution Atmospheric Pressure Chemical Ionization Mass Spectrometry (HR-APCI-MS). Two purified compounds (Dihydromikanolide and 1,3-Dicyclohexyl-4-(cyclohexylimino)-2-(cyclohexylethylamino)-3,4-dihydro-1,3-diazetium) were further evaluated for their anticancer activity against ovarian cancer cell line. Our findings depict that all the tested extracts showed considerable anticancer potential through cell viability assays. The purified compound 1 - Dihydromikanolide from methanolic extract was found to be active against ovarian cancer cells and can be explored as a promising nutra-pharmaceutical candidate against ovarian cancer. However, further studies exploring the molecular pathways and in vivo testing are required.

Phytochemical investigation and effective therapeutic potential of plants extracts against breast and ovarian cancer cell lines: compounds from zizyphus mauritiana and triticum aestivum.

ancer is the leading cause of death, accounting for approximately one out of six people dying with this disease worldwide. Among all, the breast and ovarian cancers are top-ranked causes of women mortalities compared to other disorders. Although, there is advancement in technologies, but still, there are unresolved concerns to overcome the global disease burden. Currently, plants are being explored as a natural remedy to cure disorders. This research was planned to explore phytochemicals in methanolic extracts of Zizyphus mauritiana and Triticum aestivum, and their pharmacological activities were studied through Agrobacterium tumefaciens bacteria, in vitro breast cancer cell line and ovarian cancer cell line to find out novel candidates in disease control and prevention. Eleven different types of bioactive compounds were analysed in the tested extracts. The highest crude extracts percentage (75±0.02) was observed with Z. mauritiana. The extracts showed promising cell growth inhibition and tumor initiation inhibition in potato disc assay. MTT assay and Incucytes imaging analysis revealed that Z. mauritiana extract had a higher anticancer potential with 40 ± 0.92 cell viability against breast cancer cells (SKBR3) and 45 ±0.29 against ovarian cancer cells (SKOV3). In conclusion, these extracts could be used as chemotherapeutics owing to their cheapness, and easy availability. While detailed study is required for further purification and characterization of bioactives/target compounds and in-vivo activity confirmations.

Bridging the gaps in secondary fracture prevention at a single center in Pakistan-compliance with the IOF best practice framework.

PURPOSE: The International Osteoporosis Foundation (IOF) formulated a set of best practice framework as an international benchmark for secondary fracture prevention (SFP) and fracture liaison services (FLS), delineating essential elements of service delivery. The aim of this audit was to assess compliance with the IOF standards for patients ≥ 50 years presenting with fragility hip fractures at a tertiary care center in Pakistan. METHODS: A retrospective sample of hip fracture cases from Jan 2019 to Dec 2019, treated at the section of Orthopedic Surgery, Aga Khan University, Karachi, was conducted. After excluding high energy trauma cases and patients younger than 50 years of age, medical records were audited, using a pre-structured Performa based on IOF standards. Compliance level of 0, 1, 2, and 3 was recorded as defined by IOF. Microsoft excel was used for data analysis. RESULTS: A compliance level of 3 was recorded for patient identification and fall prevention services, whereas level 1 was attained for database maintenance for 25 (100%) cases. For medication initiation, level 0 was recorded for all the cases; however, 8 (32%) cases were prescribed calcium and vitamin D supplements. For the standards, including post-fracture assessment timing, evaluation of secondary causes of osteoporosis, multifaceted assessment, medication review, communication strategy, and long-term management, a level 0 was noted for 25 (100%) cases. Moreover, no recommended assessment guidelines were followed uniformly. CONCLUSION: The care gaps identified require substantial efforts to ensure adequate implementation of the overall best practice standards for SFP, necessitating the need for FLS initiation and establishment of fracture care pathway.

Impact of COVID-19 on the pre and post analytical clinical laboratory testing processes- A performance evaluation study using six sigma.

BACKGROUND: The aim of this study was to determine the impact of COVID-19 pandemic on the total testing process using six sigma metrics based on a comparison of pre and during pandemic periods. MATERIAL & METHODS: The study duration was over 12 months, 6 months before and 6 months after the COVID-19 onset in Pakistan in March 2020 after the recognition of the first case, using quality indicators (QIs). QIs were chosen from a model of QIs recommended by the CAP. Analysis was performed using Six Sigma calculators and QIs were expressed in percentage (%) and Sigma value were computed. Three levels of performance quality i.e. 25th, 50th, and 75th percentile were derived, being best, common and worst performance respectively. Between-group differences were tested using the Mann-Whitney's U test. RESULTS: The median defect percentages of these QIs ranged from 0% to 0.27% for the pre-pandemic period and 0% to 0.13% for the during pandemic period. Meanwhile, sigma values of the majority of the QIs were all above 4.0σ during the pre and the pandemic times. For the pre-analytical phase, sigma scores declined for 1 QI, improved for 3 QIs and remained same for 2. In the post analytical phase, no change in sigma metrics was noted for critical values notification. Considerable increase in defect percentage of inappropriate turnaround times was noted. CONCLUSION: The emergency preparedness proved to be fruitful as depicted by exceptional performance on the sigma metrics for most Qis both prior to and during the pandemic. The pre-analytical and the post analytical phases, being the most error sensitive requires strict vigilance.

Structure-Based Designing, Solvent Less Synthesis of 1,2,3,4-Tetrahydropyrimidine-5-carboxylate Derivatives: A Combined In Vitro and In Silico Screening Approach.

OBJECTIVE: In this study, small molecules possessing tetrahydropyrimidine derivatives have been synthesized having halogenated benzyl derivatives and carboxylate linkage. As previously reported, FDA approved halogenated pyrimidine derivatives prompted us to synthesize novel compounds in order to evaluate their biological potential. METHODOLOGY: Eight pyrimidine derivatives have been synthesized from ethyl acetoacetate, secondary amine, aromatic benzaldehyde by adding catalytic amount of CuCl2·2H2O via solvent less Grindstone multicomponent reagent method. Molecular structure reactivity and virtual screening were performed to check their biological efficacy as an anti-oxidant, anti-cancer and anti-diabetic agent. These studies were supported by in vitro analysis and QSAR studies. RESULTS: After combined experimental and virtual screening 5c, 5g and 5e could serve as lead compounds, having low IC50 and high binding affinity.

Establishing reference interval for thyroid-stimulating hormone in children below two-year ages in Pakistani population.

INTRODUCTION: Reference intervals (RIs) of thyroid-stimulating hormone (TSH) and free thyroxine (FT4) are age, assay and population specific. Currently, the age and assay-specific RIs for TSH are not available for children under two years of age. This study aimed to establish reference intervals for serum concentrations of TSH and FT4 in healthy children aged 1-24 months as per CLSI C28-A3 guidelines. METHODS: This prospective cross-sectional study was conducted in children from 1 to 24 months visiting the clinical laboratory for serum vitamin D testing but without any recent illness, hospitalization, medication and history of maternal thyroid diseases from August 2018 to March 2019 were invited to participate in the study.Serum TSH and FT4 were measured on ADVIA Centaur (Siemens Diagnostics, US), using chemiluminescence immunoassay. Kolmogorov-Smirnov test assessed normality of the data and RIs based on central 95% of the population were established using the non-parametric approach. RESULTS: After excluding one subject with confirmed congenital hypothyroidism, a total of 131 children were included in the study. The median (IQR) age of the study subjects was 12 months (11), and majority 78 (59.5%) were boys. The RIs were established using non-parametric approach as the data was not normally distributed. Reference interval for TSH was 0.73-4.94 µIU/mL and for FT4 was 0.81-1.51 ng/dl. CONCLUSION: We established assay-specific RIs for serum TSH and FT4 in children aged 1-24 months in our population. The RIs were slightly lower from RIs developed on other platforms in different population.

A cross sectional evaluation of the corona-score for swift identification of SARS-CoV-2 infection at a tertiary care hospital in Pakistan.

BACKGROUND: The Corona-Score is one of the first and most widely used predictive model for coronavirus 2 (SARS-CoV-2) infection. The purpose of this study was to validate the performance of Corona-Score in a cohort of Pakistani patients pursuing care for suspected infection. METHODS: After seeking institution's ethical committee exemption, results of serum lactate dehydrogenase (LDH), C-reactive protein (CRP), ferritin, absolute lymphocyte and neutrophil counts, chest x-ray findings and demographics of suspected COVID-19 cases with respiratory symptoms were recouped from electronic medical record. The pre-validated score as proposed by Kurstjens S et al., was calculated. The subjects were divided into SARS-CoV-2 positive and negative on the basis of reverse transcription-polymerase chain reaction (RT-PCR) findings. Median and interquartile range (IQR) was calculated for the score in the two groups and the difference was assessed using the independent sample median test. Receiver operating characteristics (ROC) curve analysis was plotted. Statistical analyses were carried out using SPSS 26, with statistical significance set at p value < 0.05. RESULTS: A total of sixty cases, 30 (50%) RT-PCR positive and 30 (50%) negative with a median Corona-Score of 3.5 (IQR: 0-6) and 1.5 (IQR: 0-4) respectively, were evaluated. A p-value of 0.61 showing no statistically significant between group differences was observed. The area under the curve of Corona-Score in our population of patients was 0.59 (95% CI: 0.45-0.74). Using the cut-off values of four originally identified by Kurstjens et al. the model displayed 43.3% sensitivity and 70% specificity with an overall accuracy of 56.67%. CONCLUSION: Corona-Score displayed a lower diagnostic accuracy which may be attributable to the different genetic framework, viral strain and severity of the disease in Pakistanis compared to the population where this score was originally validated. However, large multi-center studies across the country are dire need of time to evaluate the score in overly exhausted health care setup and limited availability of PCR testing.

Diagnostic Accuracy of the Forns Score for Liver Cirrhosis in Patients With Chronic Viral Hepatitis.

Introduction Liver cirrhosis is an irreversible and end-stage disease. It results from chronic liver damage characterized by the replacement of normal liver tissue by fibrosis, leading to the progressive loss of liver function. Making an early diagnosis of cirrhosis is important for patients with chronic hepatitis because early antiviral therapy can prevent the progression of cirrhosis and even induce regression. There have been efforts to develop surrogate markers for liver cirrhosis as the biopsy is invasive, costly, and difficult to standardize. Methods This was a cross-sectional study conducted at the Section of Chemical Pathology, the Department of Pathology and Laboratory Medicine in Collaboration with the Section of Gastroenterology, Department of Medicine, the Aga Khan University, from January to December 2018. A total of 90 patients (>18 years of age) with a history of chronic viral hepatitis, who were attending the FibroScan® (Echosens, Paris, France) clinic were included. Patients with a history of autoimmune liver diseases and hepatocellular carcinoma were excluded from the study. Blood samples withdrawn were analyzed on ADVIA Centaur® (Siemens Healthineers, Erlangen, Germany), and Forns scores were calculated based on the following four parameters: patient age, total cholesterol, gamma-glutamyl transferase (GGT), and platelet count. Results The median age of the patients was 38.5 years [interquartile range (IQR): 21]. Among the study population, 59 (65.6%) were males and 31 (34.4%) were females; 26 patients showed reactivity for hepatitis B surface antigen (HBsAg), and 63 patients were found chronic with hepatitis C virus (HCV). The proportion of HCV was observed to be higher as compared with that of Hepatitis B virus (HBV). Nineteen patients were found to have jaundice and only one patient had ascites. An Area Under the Receiver Operating Curve (AUROC) was generated to determine the diagnostic accuracy of the Forns score. It was observed that the Forn score value of >7.110 had an AUROC of 0.9928 (95% CI: 0.9821-1.003, p-value: <0.001) with a sensitivity of 100% (95% CI: 91.19-100.0%) and specificity of 94% (95% CI: 83.45-98.75%), with a higher positive likelihood ratio of 16.67. Conclusion This study found the Forns score to be sensitive and specific in diagnosing liver cirrhosis in patients with chronic hepatitis. The Forns score at a cutoff of 7.11 is highly sensitive as well as a specific noninvasive method that can be used to ascertain the status of fibrosis in chronic hepatitis patients.

Evaluation of serum ferritin for prediction of severity and mortality in COVID-19- A cross sectional study.

BACKGROUND: Ferritin even though widely recognized as a representative of total body iron stores, its prognostic utility is linked with COVID-19. This study was aimed at evaluation of the association of ferritin with severity in Coronavirus disease 2019 (COVID-19), hospitalized patients and to test the hypothesis that it is an independent predictor of mortality. MATERIAL AND METHODS: This study was conducted at Chemical Pathology, Department of Pathology and Laboratory Medicine, Aga Khan University (AKU), Karachi. Medical records of all in-patients including both genders, and all age groups with documented COVID-19 from 1st March to 10th August 2020 were reviewed. The subjects were divided into two categories severe and non-severe COVID-19; and survivors and non-survivors. The details were recorded on a pre-structured performa. Between-group differences were tested using the Mann-Whitney's U-test. The receiver operating characteristic curve was plotted for ferritin with severity and mortality. A binary logistic regression was used to identify variables independently associated with mortality. The data was analyzed using Statistical Package for the Social Sciences (SPSS). RESULTS: A total of 336 in patients were reviewed as declared COVID-19 positive during the study duration, and 157 were included in the final analysis including 108 males and 49 females. Statistically significant difference in ferritin was found in the two categories based on severity and mortality. Binary logistic regression showed ferritin to be an independent predictor of all-cause mortality supplemented with an AUC of 0.69 on ROC analysis. CONCLUSIONS: Serum ferritin concentration is a promising predictor of mortality in COVID-19 cases.

Hajdu Cheney Syndrome due to NOTCH2 defect - First case report from Pakistan and review of literature.

INTRODUCTION AND IMPORTANCE: Hajdu Cheney Syndrome (HCS) is a rare skeletal disease characterized by severe, progressive focal bone loss with osteoporosis, variable craniofacial, vertebral anomalies and distinctive facial features. It is inherited as an autosomal dominant disease although sporadic cases have been described in literature. Identifying these cases in clinical practice is important for proper diagnosis and management. CASE PRESENTATION: We report a case of a 36-year-old male patient presented at metabolic bone disease clinic at the Aga Khan University Hospital with history of multiple fragility fractures and juvenile osteoporosis since childhood. DNA sequence analysis of the NOTCH2 coding sequence revealed a pathogenic variant in NOTCH 2, Exon 34, c.6426_6427insTT (p.Glu2143Leufs*5), consistent with a NOTCH2 related conditions including HCS. CLINICAL DISCUSSION: The multitude of presentations associated with HCS are linked to the NOTCH2 gene, as Notch signaling is one of the core signaling pathways that control embryonic development. Hence, mutations in the Notch signaling pathway cause developmental phenotypes that affect various organs including the liver, skeleton, heart, eye, face, kidney, and vasculature. CONCLUSION: To the best of our knowledge, nucleotide mutations of c.6933delT, c.6854delA, c.6787C.T, and c.6424-6427delTCTG were all determined to be novel, with c.6428T > C being the most common mutation found in literature. The c.6426_6427insTT mutation our patient was found to have via gene sequencing too appears to be a novel mutation, which has not previously been reported in literature.

Trend analysis of lab tests requisitions of COVID-19 prognostic biomarkers at a clinical chemistry reference laboratory-an observational study.

BACKGROUND: Biochemical parameters, such as C-reactive protein (C-RP), Procalcitonin (PCT), Lactate dehydrogenase (LDH) and Ferritin are associated with COVID-19 severity and prognosis. This trend analysis of COVID-19 prognostic biomarker requisitions is aimed at providing a reflection of the clinical practices adopted amidst the peak of the pandemic. This knowledge of the prognostic biomarkers utilized, will further aid to classify patients based on their risk, for optimal resource allocation and improve outcomes. MATERIAL & METHODS: This cross-sectional study was conducted at the clinical chemistry laboratory at the Aga Khan University Hospital (AKUH), Karachi Pakistan. A team consisting of two clinical chemistry consultants reviewed the COVID-19 prognostic biomarkers tests performance data from March to July 2020 using the integrated laboratory information management system (ILMS). The test statistics of March to July 2020 when COVID-19 cases were on the rise in the country were compared with those of the same months from 2019. The changes in the test groups were expressed in percentages. Microsoft Excel for windows 2019 was used for data analysis. RESULTS: The total specimens received for testing in 2020 (n = 574,092) showed a percent decline of approximately (-) 33% compared to 2019 (n = 858,756). Contrary to the overall decline in volumes an upward surge was noted for the prognostic biomarkers. From March to July, the highest percent change was noted for LDH (+155.1%), followed by PCT (+66.7.1%), C-RP (+26.5%) and Ferritin (+22.1%) in 2020 compared to the same time frame in 2019. The highest percent change was noted in June. CONCLUSION: During the COVID 19 pandemic, a significant increase in utilization of laboratory services was seen for COVID-19 prognostic markers.