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Ghulam U, Nazim F, Farooqui N, Rizwan-ul-Hasan S, Anwar MF, Ahmed K, Jamal A, Kayani HA, Mughal N, Hussain A, Sarria-Santamera A, Abidi SH. Analysis of differential gene expression of pro-inflammatory cytokines in the nasopharyngeal milieu of mild & severe COVID-19 cases. PLoS One 2022; 17:e0279270. [PMID: 36584119 PMCID: PMC9803207 DOI: 10.1371/journal.pone.0279270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 12/02/2022] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION A subset of individuals with COVID-19 can suffer from a severe form of the disease requiring breathing support for respiratory failure and even death due to disease complications. COVID-19 disease severity can be attributed to numerous factors, where several studies have associated changes in the expression of serum pro-inflammatory cytokines with disease severity. However, very few studies have associated the changes in expression of pro-inflammatory changes in the nasopharyngeal milieu with disease severity. Therefore, in the current study, we performed differential gene expression analysis of various pro-inflammatory cytokines in the nasopharyngeal milieu of mild & severe COVID-19 cases. MATERIAL AND METHOD For this retrospective, cross-sectional study, a total of 118 nasopharyngeal swab samples, previously collected from mild and severe (based on the WHO criteria) COVID-19 patients were used. A real-time qPCR was performed to determine the viral loads and also evaluate the mRNA expression of eight cytokines (IL-1, IL-2, IL-4, IL-6, IL-10, IFN-γ, TGF-β1, and TNF-α). Subsequently, an unpaired T-test was applied to compare the statistical difference in mean expression of viral loads and each cytokine between the mild and severe groups, while the Pearson correlation test was applied to establish a correlation between disease severity, viral load, and cytokines expression. Similarly, a multivariable logistic regression analysis was performed to assess the relationship between different variables from the data and disease severity. RESULTS Out of 118 samples, 71 were mild, while 47 were severe. The mean viral load between the mild and severe groups was comparable (mild group: 27.07± 5.22; severe group: 26.37 ±7.89). The mRNA expression of cytokines IL-2, IL-6, IFN- γ, and TNF-α was significantly different in the two groups (p<0.05), where the Log2 normalized expression of IL-2, IL-6, IFN- γ, and TNF-α was found to be 2.2-, 16-, 2.3-, and 1.73-fold less in the severe group as compared to the mild group. Furthermore, we also observed a significant positive correlation between all the cytokines in the severe group. The multivariate analysis showed a significant relationship between age, IL-6, and disease severity. CONCLUSION This decreased expression of certain cytokines (IL-2, IL-6, TNF-α, and IFN-γ) in the nasopharyngeal milieu may be considered early biomarkers for disease severity in COVID-19 patients.
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Affiliation(s)
- Unzela Ghulam
- Department of Biosciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Karachi, Pakistan
| | - Fizza Nazim
- Department of Biosciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Karachi, Pakistan
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Nida Farooqui
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | | | - Muhammad Faraz Anwar
- Department of Biochemistry, Bahria University Medical & Dental College, Karachi, Pakistan
| | - Khalid Ahmed
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Abid Jamal
- Cancer Foundation Hospital, Karachi, Pakistan
| | - Hammad Afzal Kayani
- Department of Biosciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Karachi, Pakistan
| | - Nouman Mughal
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Surgery, Aga Khan University, Karachi, Pakistan
| | - Azhar Hussain
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | | | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
- Department of Biomedical Sciences, Nazarbayev University School of Medicine, Astana, Kazakhstan
- * E-mail:
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Farooqui N, Mir F, Siddiqui D, Hotwani A, Nathwani AA, Mahmood SF, Sadiq K, Kayani HA, Sheikh SA, Shah SA, Ferrand RA, Abidi SH. Phylogenetic and drug- and vaccine-resistance profiles of Hepatitis B Virus among children with HIV co-infection in Pakistan. Infect Genet Evol 2022; 105:105371. [PMID: 36179949 PMCID: PMC9614405 DOI: 10.1016/j.meegid.2022.105371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 02/07/2023]
Abstract
INTRODUCTION HIV-1 and hepatitis B virus (HBV) share common routes of transmission and therefore co-infection is common. In 2019, an HIV-1 outbreak that resulted in >1000 children being infected, predominantly through nosocomial transmission, occurred in Sindh, Pakistan. We conducted a phylogenetic and drug resistance analysis of the HBV Reverse Transcriptase (RT) gene in children with HIV-1 and HBV co-infection. METHODOLOGY Blood samples were collected from 321 children with HIV who were recruited as part of a study to investigate the HIV-1 outbreak. All samples were tested for HBV surface antigen (HBsAg) using an ELISA assay, and positive samples were used to amplify and sequence the HBV RT gene. The phylogenetic relationship between sequences was analyzed, and drug- and vaccine- resistance mutations in the RT gene were explored. RESULTS Of 321 samples, 23% (n = 75) were positive for HBsAg on ELISA. Phylogenetic analysis of the sequences revealed that 63.5% of HBV sequences were sub-genotype D1, while the rest were sub-genotype D2. Cluster analysis revealed grouping of sub-genotype D1 sequences exclusively with Pakistani sequences, while clustering of sub-genotypes D2 predominantly with global sequences. The 236Y mutation associated with resistance to tenofovir was observed in 2.8% of HBV sequences. Additionally, seven vaccine escape mutations were observed, the most common being 128 V. CONCLUSION Our study suggests ongoing transmission of HBV D1 and D2 sub-genotypes in the HIV-1 co-infected population, likely nosocomially, given common routes of HVB and HIV-1 transmission. The prevalence of major HBV drug- and vaccine-resistant mutations remains low. Surveillance for further transmissions and the possible emergence of major drug- or vaccine-resistant variants is required.
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Affiliation(s)
- Nida Farooqui
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan; Department of Biosciences, The Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Karachi, Pakistan
| | - Fatima Mir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Dilsha Siddiqui
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Apsara Ali Nathwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Kamran Sadiq
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Hammad Afzal Kayani
- Department of Biosciences, The Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Karachi, Pakistan
| | | | | | - Rashida Abbas Ferrand
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan; Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan; Department of Biomedical Sciences, Nazarbayev University School of Medicine, Nur-Sultan, Kazakhstan.
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Adnan Y, Ali SMA, Awan MS, Idress R, Awan MO, Farooqui HA, Kayani HA. Hormone receptors AR, ER, PR and growth factor receptor Her-2 expression in oral squamous cell carcinoma: Correlation with overall survival, disease-free survival and 10-year survival in a high-risk population. PLoS One 2022; 17:e0267300. [PMID: 35544472 PMCID: PMC9094515 DOI: 10.1371/journal.pone.0267300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 04/06/2022] [Indexed: 11/18/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) comprises most of head and neck neoplasms and is one of the highest-ranking and lethal cancers in Pakistan due to prevailing mouth habits. Several types of receptors act as prognostic markers and targets for therapy in some cancers, but their application in OSCC is largely unexplored. This study aimed to evaluate the expression of hormonal receptors and Her-2 in OSCC patients and correlate it with 10-year, overall and disease-free survival. To achieve this objective, immunohistochemistry for Her-2, AR, ER and PR was performed on 100 formalin-fixed paraffin-embedded primary OSCC specimens. Receptor expression was correlated with mouth habits and clinicopathological features and patient survival was analyzed using Kaplan-Meier method and Cox regression univariate analysis. We observed that in 100 patients, there were 57 males and 43 females. Immunopositive Her-2 expression was observed in 21% of patients, AR in 13%, ER in 3% and 0% for PR. Patients with betel quid/areca nut mouth habits had significantly absent Her-2 expression (P = 0.035). Also, Her-2 negative patients were also negative for AR expression (P = 0.002). Her-2 positive patients had poor 10-year survival (P = 0.041). A trend of low survival and high recurrence rate was observed in AR positive patients, but this was not significant (P = 0.072). No statistically relevant correlations were seen in the case of ER and PR. In conclusion, Her-2 may be a valuable marker for predicting long-term prognosis of OSCC patients.
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Affiliation(s)
- Yumna Adnan
- Office of Academia and Research in Surgery, Department of Surgery, Aga Khan University Hospital, Karachi, Pakistan
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Karachi, Pakistan
| | - Syed Muhammad Adnan Ali
- Office of Academia and Research in Surgery, Department of Surgery, Aga Khan University Hospital, Karachi, Pakistan
- * E-mail:
| | - Muhammad Sohail Awan
- Section of Otolaryngology–Head and Neck Surgery, Department of Surgery, Aga Khan University Hospital, Karachi, Pakistan
| | - Romana Idress
- Section of Histopathology, Department of Pathology and Laboratory Medicines, Aga Khan University Hospital, Karachi, Pakistan
| | | | - Hasnain Ahmed Farooqui
- Office of Academia and Research in Surgery, Department of Surgery, Aga Khan University Hospital, Karachi, Pakistan
| | - Hammad Afzal Kayani
- Department of Biosciences, Faculty of Life Sciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Karachi, Pakistan
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Adnan Y, Ali SMA, Awan MS, Zahid N, Awan MO, Afzal Kayani H, Farooqui HA. Body Mass Index and Diabetes Mellitus May Predict Poorer Overall Survival of Oral Squamous Cell Carcinoma Patients: A Retrospective Cohort From a Tertiary-Care Centre of a Resource-Limited Country. Clin Med Insights Oncol 2022; 16:11795549221084832. [PMID: 35342323 PMCID: PMC8943457 DOI: 10.1177/11795549221084832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 02/15/2022] [Indexed: 11/27/2022] Open
Abstract
Introduction: Oral squamous cell carcinoma (OSCC) is one of the highest-ranking cancers
among both genders in Pakistan. Obesity is linked to a much higher risk for
developing multiple cancer types. Individuals with Diabetes mellitus (DM)
face an increased risk for developing oral cancer. Hence, the objective of
this study was to identify the effect of obesity and DM on the prognosis of
OSCC patients. Methods: This retrospective cohort analysis was conducted on 386 patients diagnosed
and treated for OSCC at The Aga Khan University Hospital, Karachi, Pakistan.
Patient information was obtained from hospital medical records. Obesity was
defined as having a body mass index (BMI) of ⩾25 kg/m2 according
to the WHO Asian cut-offs for BMI. Patient BMI was correlated with diabetes
status, clinicopathological features and overall survival. Kaplan-Meier
survival analysis was performed, along with univariate and multivariate cox
regression analysis to test the effect of obesity and diabetes on overall
survival. Results: In a set of 386 patients, there were 296 males (76.7%) and 90 females
(23.3%). The mean BMI was 24.4 (SD ± 5.25) and 42.7% of patients were found
to be obese (⩾25 BMI). 64 patients (16.6%) were diabetic. The risk of death
was significantly higher in underweight patients (P = .035)
compared with normal weight individuals. Diabetics had a higher mean BMI
compared with non-diabetics. However, DM was not a statistically valid
predictor of survival. Conclusion: Underweight OSCC patients were at a higher risk of death compared with normal
weight OSCC patients.
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Affiliation(s)
- Yumna Adnan
- Office of Academia and Research in Surgery, Department of Surgery, The Aga Khan University Hospital, Karachi, Pakistan
- Department of Biosciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Karachi, Pakistan
| | - Syed Muhammad Adnan Ali
- Office of Academia and Research in Surgery, Department of Surgery, The Aga Khan University Hospital, Karachi, Pakistan
| | - Muhammad Sohail Awan
- Section of Otolaryngology, Head & Neck Surgery, Department of Surgery, The Aga Khan University Hospital, Karachi, Pakistan
| | - Nida Zahid
- Office of Academia and Research in Surgery, Department of Surgery, The Aga Khan University Hospital, Karachi, Pakistan
| | | | - Hammad Afzal Kayani
- Department of Biosciences, Shaheed Zulfikar Ali Bhutto Institute of Science and Technology, Karachi, Pakistan
| | - Hasnain Ahmed Farooqui
- Office of Academia and Research in Surgery, Department of Surgery, The Aga Khan University Hospital, Karachi, Pakistan
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Muneer S, Kayani HA, Ali K, Asif E, Zohra RR, Kabir F. Laboratory biosafety and biosecurity related education in Pakistan: Engaging students through the Socratic method of learning. Journal of Biosafety and Biosecurity 2021. [DOI: 10.1016/j.jobb.2021.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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