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Qadir M, Faryal R, Khan MT, Khan SA, Zhang S, Li W, Wei DQ, Tahseen S, McHugh TD. Phenotype versus genotype discordant rifampicin susceptibility testing in tuberculosis: implications for a diagnostic accuracy. Microbiol Spectr 2024; 12:e0163123. [PMID: 37982632 PMCID: PMC10783056 DOI: 10.1128/spectrum.01631-23] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/10/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE An accurate diagnosis of drug resistance in clinical isolates is an important step for better treatment outcomes. The current study observed a higher discordance rate of rifampicin resistance on Mycobacteria Growth Indicator Tube (MGIT) drug susceptibility testing (DST) than Lowenstein-Jenson (LJ) DST when compared with the rpoB sequencing. We detected a few novel mutations and their combination in rifampicin resistance isolates that were missed by MGIT DST and may be useful for the better management of tuberculosis (TB) treatment outcomes. Few novel deletions in clinical isolates necessitate the importance of rpoB sequencing in large data sets in geographic-specific locations, especially high-burden countries. We explored the discordance rate on MGIT and LJ, which is important for the clinical management of rifampicin resistance to avoid the mistreatment of drug-resistant TB. Furthermore, MGIT-sensitive isolates may be subjected to molecular methods of diagnosis for further confirmation and treatment options.
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Affiliation(s)
- Mehmood Qadir
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Rani Faryal
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Tahir Khan
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, China
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, Lahore, Pakistan
| | - Sajjad Ahmed Khan
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
| | - Shulin Zhang
- School of Medicine, Department of Immunology and Microbiology, Shanghai Jiao Tong University, Shanghai, China
| | - Weimin Li
- National Tuberculosis Clinical Lab of China, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Dong Qing Wei
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, Henan, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Peng Cheng Laboratory, Shenzhen, Guangdong, China
| | - Sabira Tahseen
- National TB Control Program, National TB Reference Laboratory, Islamabad, Pakistan
| | - Timothy D. McHugh
- Centre for Clinical Microbiology, University College London, London, United Kingdom
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2
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Mushtaq S, Khan MIU, Khan MT, Lodhi MS, Wei DQ. Novel mutations in structural proteins of dengue virus genomes. J Infect Public Health 2023; 16:1971-1981. [PMID: 37879150 DOI: 10.1016/j.jiph.2023.10.005] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 09/01/2023] [Accepted: 10/02/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Genomic characterization of the dengue virus (DENV) is useful for understanding its molecular evolution, transmission, pathogenicity and infectivity. The DENV genomic RNA encodes three structural proteins, capsid (C) envelope (E) and membrane (M) proteins mediating viral entry and assembly during host infection. The current study aims to explore the DENV serotypes and mutations in the E and M proteins. METHODS Twenty-three samples of DENV-positive patients were processed and selected for whole genome sequencing (WGS) from the Punjab Province of Pakistan. RESULTS Among the 23 WGS, 19 samples showed numerous mutations (BioProject ID PRJNA943555). DENV1 and DENV2 are the most prevalent serotypes. A total of 179 mutations were detected in the E protein, in which K203E, T88A, I114L, and I293T are novel. The I270L, T272A, S273L, and T277A were found in the "kl" β-hairpin (aa 270-279). The M protein harbors 74 mutations, of which 24 were novel. Three prominent complementary regions in the prM and E protein complex formations include R6, E46, D47, D63, and D65 on 'pr' peptide, and E84, K64, and H244, K247 on E, remain conserved except R6C. To our knowledge, it is the first comprehensive study of mutations in structural proteins. CONCLUSION Genomic epidemiology is critical for analyzing emerging mutations and designing new policies therapeutic efforts for future outbreaks.
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Affiliation(s)
- Saira Mushtaq
- Institute of Molecular Biology and Biotechnology, The University of Lahore, KM Defence Road, Postal code: 5881, Lahore, Pakistan.
| | - Malik Ihsan Ullah Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, KM Defence Road, Postal code: 5881, Lahore, Pakistan.
| | - Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, KM Defence Road, Postal code: 5881, Lahore, Pakistan; Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, Henan 473006, PR China.
| | - Madeeha Shahzad Lodhi
- Institute of Molecular Biology and Biotechnology, The University of Lahore, KM Defence Road, Postal code: 5881, Lahore, Pakistan.
| | - Dong Qing Wei
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, Henan 473006, PR China; State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, PR China; Peng Cheng Laboratory, Shenzhen, Guangdong 518055, PR China.
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3
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Khan A, Shahab M, Nasir F, Waheed Y, Alshammari A, Mohammad A, Zichen G, Li R, Wei DQ. Exploring the Traditional Chinese Medicine (TCM) database chemical space to target I7L protease from monkeypox virus using molecular screening and simulation approaches. SAR QSAR Environ Res 2023; 34:689-708. [PMID: 37675795 DOI: 10.1080/1062936x.2023.2250723] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/16/2023] [Indexed: 09/08/2023]
Abstract
In the current study, we used molecular screening and simulation approaches to target I7L protease from monkeypox virus (mpox) from the Traditional Chinese Medicines (TCM) database. Using molecular screening, only four hits TCM27763, TCM33057, TCM34450 and TCM31564 demonstrated better pharmacological potential than TTP6171 (control). Binding of these molecules targeted Trp168, Asn171, Arg196, Cys237, Ser240, Trp242, Glu325, Ser326, and Cys328 residues and may affect the function of I7L protease in in vitro assay. Moreover, molecular simulation revealed stable dynamics, tighter structural packing and less flexible behaviour for all the complexes. We further reported that the average hydrogen bonds in TCM27763, TCM33057, TCM34450 and TCM31564I7L complexes remained higher than the control drug. Finally, the BF energy results revealed -62.60 ± 0.65 for the controlI7L complex, for the TCM27763I7L complex -71.92 ± 0.70 kcal/mol, for the TCM33057I7L complex the BF energy was -70.94 ± 0.70 kcal/mol, for the TCM34450I7L the BF energy was -69.94 ± 0.85 kcal/mol while for the TCM31564I7L complex the BF energy was calculated to be -69.16 ± 0.80 kcal/mol. Although, we used stateoftheart computational methods, these are theoretical insights that need further experimental validation.
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Affiliation(s)
- A Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nayang, P.R. China
- School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia
| | - M Shahab
- State Key Laboratory of Chemical Resources Engineering, Beijing University of Chemical Technology, Beijing, China
| | - F Nasir
- Amna Inayat Medical College, Lahore, Pakistan
| | - Y Waheed
- Office of Research, Innovation, and Commercialization (ORIC), Shaheed Zulfiqar Ali Bhutto Medical University (SZABMU), Islamabad, Pakistan
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - A Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - A Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait
| | - G Zichen
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - R Li
- Department of Flowers, college of Horticulture, China Agriculture University, Beijing, P.R. China
| | - D Q Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nayang, P.R. China
- Peng Cheng Laboratory, Vanke Cloud City, Shenzhen, P.R China
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4
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Lodhi MS, Khan MT, Aftab S, Samra ZQ, Wang H, Wei DQ. A novel formulation of theranostic nanomedicine for targeting drug delivery to gastrointestinal tract cancer. Cancer Nanotechnol 2021. [DOI: 10.1186/s12645-021-00098-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Abstract
Background
Theranostic nanomedicines contain a nanovehicle that has fluorescent properties and can be used for diagnostic, therapeutic and prognostic purposes. The transferrin receptor expression is 1000-fold higher in rapidly growing cancer cells as compared to the normal cells and, therefore, can be used in targeted drug delivery systems. The objective of the present study was to design a novel targeted gold nanoparticle (GNPs)-based theranostic formulation for gastrointestinal (GI) tract-related cancers. The synthesized GNPs were conjugated to transferrin and doxorubicin both separately and collectively to check their cytotoxic properties. The in vitro cytotoxicity of nanocomposites was observed against colon cancer cell line HCT-116. The doxorubicin conjugated nanocomposites showed almost the same cytotoxicity, but more effect at later hours (h). The IC50 and IC100 were 50 µg/ml and 250 µg/ml, respectively, equivalent to the doxorubicin weight for GNP theranostic nanomedicine.
Results
The maximum effect was observed after 12 h and nanomedicines were still active after 72 h of treatment. Our in vivo data proved that nanomedicine crossed all the barriers and was successfully delivered to the tumour cells. Theranostic nanomedicine’s (TNM) effect on body weight and survival rate on mice was many folds better than mice in pure doxorubicin group. It also showed almost 80% survival rate on day 40. The in vivo and in vitro results show the effects of prolonged drug release and the nanomedicine was not toxic to vital organs of the animal.
Conclusion
This is one of its kind studies in which a novel targeted nanomedicines approach was formulated for therapeutic as well as prognostic purposes against GI tract cancer.
Graphic Abstract
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5
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Mou K, Abdalla M, Wei DQ, Khan MT, Lodhi MS, Darwish DB, Sharaf M, Tu X. Emerging mutations in envelope protein of SARS-CoV-2 and their effect on thermodynamic properties. Inform Med Unlocked 2021; 25:100675. [PMID: 34337139 PMCID: PMC8314890 DOI: 10.1016/j.imu.2021.100675] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/11/2021] [Accepted: 07/19/2021] [Indexed: 12/23/2022] Open
Abstract
Structural proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are potential drug targets due to their role in the virus life cycle. The envelope (E) protein is one of the structural proteins; plays a critical role in virulency. However, the emergence of mutations oftenly leads to drug resistance and may also play a vital role in virus stabilization and evolution. In this study, we aimed to identify mutations in E proteins that affect the protein stability. About 0.3 million complete whole genome sequences were analyzed to screen mutations in E protein. All these mutations were subjected to stability prediction using the DynaMut server. The most common mutations that were detected at the C-terminal domain, Ser68Phe, Pro71Ser, and Leu73Phe, were examined through molecular dynamics (MD) simulations for a 100ns period. The sequence analysis shows the existence of 259 mutations in E protein. Interestingly, 16 of them were detected in the DFLV amino acid (aa) motif (aa72-aa75) that binds the host PALS1 protein. The results of root mean square deviation, fluctuations, radius of gyration, and free energy landscape show that Ser68Phe, Pro71Ser, and Leu73Phe are exhibiting a more stabilizing effect. However, a more comprehensive experimental study may be required to see the effect on virus pathogenicity. Potential antiviral drugs, and vaccines may be developed used after screening the genomic variations for better management of SARS-CoV-2 infections.
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Affiliation(s)
- Kejie Mou
- Department of Neurosurgery, Bishan Hospital of Chongqing, Chongqing, China
| | - Mohnad Abdalla
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Pharmaceutics, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 Cultural West Road, Shandong Province, 250012, PR China
| | - Dong Qing Wei
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, PR China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, PR China
| | - Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore, Pakistan, 58810
| | - Madeeha Shahzad Lodhi
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore, Pakistan, 58810
| | - Doaa B Darwish
- Department of Biology, Faculty of Science, University of Tabuk, 71491, Saudi Arabia
| | - Mohamed Sharaf
- Department of Biochemistry and Molecular Biology, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003, PR China
- Department of Biochemistry, Faculty of Agriculture, AL-Azhar University, Nasr City, Cairo, 11751, Egypt
| | - Xudong Tu
- Chongqing Medical and Pharmaceutical College, Chongqing, China
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6
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Khan MT, Ali S, Khan AS, Ali A, Khan A, Kaushik AC, Irfan M, Chinnasamy S, Zhang S, Zhang YJ, Cui Z, Wei AJ, Wang Y, Zhao M, Liu K, Wang H, Zeb MT, Wei DQ. Insight into the drug resistance whole genome of Mycobacterium tuberculosis isolates from Khyber Pakhtunkhwa, Pakistan. Infect Genet Evol 2021; 92:104861. [PMID: 33862292 DOI: 10.1016/j.meegid.2021.104861] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/31/2021] [Accepted: 04/08/2021] [Indexed: 12/17/2022]
Abstract
Whole genome sequencing (WGS) is one of the most reliable methods for detection of drug resistance, genetic diversity in other virulence factor and also evolutionary dynamics of Mycobacterium tuberculosis complex (MTBC). First-line anti-tuberculosis drugs are the major weapons against Mycobacterium tuberculosis (MTB). However, the emergence of drug resistance remained a major obstacle towards global tuberculosis (TB) control program 2030, especially in high burden countries including Pakistan. To overcome the resistance and design potent drugs, genomic variations in drugs targets as well as in the virulence and evolutionary factors might be useful for better understanding and designing potential inhibitors. Here we aimed to find genomic variations in the first-line drugs targets, along with other virulence and evolutionary factors among the circulating isolates in Khyber Pakhtunkhwa, Pakistan. Samples were collected and drug susceptibility testing (DST) was performed as per WHO standard. The resistance samples were subjected to WGS. Among the five whole genome sequences, three samples (NCBI BioProject Accession: PRJNA629298, PRJNA629388) harbored 1997, 1162, and 2053 mutations. Some novel mutations have been detected in drugs targets. Similarly, numerous novel variants have also been detected in virulency and evolutionary factors, PE, PPE, and secretory system of MTB isolates. Exploring the genomic variations among the circulating isolates in geographical specific locations might be useful for future drug designing. To the best of our knowledge, this is the first study that provides useful data regarding the insight genomic variations in virulency, evolutionary factors including ESX and PE/PPE as well as drug targets, for better understanding and management of TB in a WHO declared high burden country.
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Affiliation(s)
- Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Sajid Ali
- Department of Microbiology, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Anwar Sheed Khan
- Department of Microbiology, Kohat University of Science and Technology and Provincial Tuberculosis Reference Laboratory, Peshawar, Pakistan.
| | - Arif Ali
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Abbas Khan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China.
| | | | - Muhammad Irfan
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, FL, USA.
| | - Sathishkumar Chinnasamy
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Shulin Zhang
- Department of Immunology and Microbiology, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
| | - Yu-Juan Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing, China.
| | - Zhilei Cui
- Zhilei Cui, Department of Respiratory Medicine, XinHua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Amie Jinghua Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Yanjie Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China
| | - Mingzhu Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Kejia Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Heng Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China.
| | - Muhammad Tariq Zeb
- Khyber Medical University and Senior Research Officer, In-charge Genomic Laboratory, Veterinary Research Institute, Peshawar 25000, Pakistan
| | - Dong Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, and Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Ministry of Education, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China; Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nanshan District, Shenzhen, Guangdong 518055, China.
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Khan MT, Ali S, Khan AS, Muhammad N, Khalil F, Ishfaq M, Irfan M, Al-Sehemi AG, Muhammad S, Malik A, Khan TA, Wei DQ. SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. ACS Omega 2021; 6:6588-6599. [PMID: 33748571 PMCID: PMC7944396 DOI: 10.1021/acsomega.0c05163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/05/2021] [Indexed: 05/08/2023]
Abstract
Among viral outbreaks, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is one of the deadliest ones, and it has triggered the global COVID-19 pandemic. In Pakistan, until 5th September 2020, a total of 6342 deaths have been reported, of which 1255 were from the Khyber Pakhtunkhwa (KPK) province. To understand the disease progression and control and also to produce vaccines and therapeutic efforts, whole genome sequence analysis is important. In the current investigation, we sequenced a single sample of SARS-CoV-2 genomes (accession no. MT879619) from a male suspect from Peshawar, the KPK capital city, during the first wave of infection. The local SARS-CoV-2 strain shows some unique characteristics compared to neighboring Iranian and Chinese isolates in phylogenetic tree and mutations. The circulating strains of SARS-CoV-2 represent an intermediate evolution from China and Iran. Furthermore, eight complete whole genome sequences, including the current Pakistani isolates which have been submitted to Global Initiative on Sharing All Influenza Data (GSAID), were also investigated for specific mutations and characters. Some novel mutations [NSP2 (D268del), NSP5 (N228K), and NS3 (F105S)] and specific characters have been detected in the coding regions, which may affect viral transmission, epidemiology, and disease severity. The computational modeling revealed that a majority of these mutations may have a stabilizing effect on the viral protein structure. In conclusion, the genome sequencing of local strains is important for better understanding the pathogenicity, immunogenicity, and epidemiology of causative agents.
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Affiliation(s)
- Muhammad Tahir Khan
- Institute of Molecular
Biology and Biotechnology (IMBB), The University
of Lahore, KM Defence Road, Lahore 58810, Pakistan
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
| | - Sajid Ali
- Department of Microbiology, Quaid-i-Azam University Islamabad, Islamabad 45320, Pakistan
| | - Anwar Sheed Khan
- Department of Microbiology, Kohat University of Science and Technology, Bannu Road, Near Jarma Bridge, Kohat 26000, Pakistan
| | - Noor Muhammad
- Department of Microbiology, Kohat University of Science and Technology, Bannu Road, Near Jarma Bridge, Kohat 26000, Pakistan
| | - Faiza Khalil
- Department of Biochemistry, Khyber Medical
College, Peshawar 25160, Pakistan
- University
of Peshawar, Road No.
2, Rahat Abad, Peshawar 25120, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Ishfaq
- Centre for Omic Sciences, Islamia
College Peshawar. Grand Trunk Road, Rahat Abad, Peshawar 25120, Pakistan
| | - Muhammad Irfan
- Department
of Oral Biology, College of Dentistry, University
of Florida, Gainesville, Florida 32611, United States
| | - Abdullah G. Al-Sehemi
- Research Center for Advanced Materials
Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Shabbir Muhammad
- Research Center for Advanced Materials
Science (RCAMS), King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- Department of Chemistry, College of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi Arabia
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
| | - Arif Malik
- Institute of Molecular
Biology and Biotechnology (IMBB), The University
of Lahore, KM Defence Road, Lahore 58810, Pakistan
| | - Taj Ali Khan
- Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Phase V, Hayatabad, Peshawar, Khyber Pakhtunkhwa 25000, Pakistan
| | - Dong Qing Wei
- State Key Laboratory of Microbial Metabolism,
Shanghai−Islamabad−Belgrade Joint Innovation Center
on Antibacterial Resistances, Joint International Research Laboratory
of Metabolic & Developmental Sciences and School of Life Sciences
and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, P. R. China
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong 518055, P. R. China
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Wei YK, Jia LQ, Fang YY, Wang LJ, Qian ZX, Yuan JN, Selvaraj G, Ji GF, Wei DQ. Formation and superconducting properties of predicted ternary hydride
ScYH
6
under pressures. Int J Quantum Chem 2020. [DOI: 10.1002/qua.26459] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yong Kai Wei
- College of Science Henan University of Technology Zhengzhou China
| | - Liang Quan Jia
- Department of Information Engineering Huzhou University Huzhou China
| | - Yan Yan Fang
- Pediatric Intensive Care Unit The First Affiliated Hospital of Zhengzhou University Zhengzhou China
| | - Long Jun Wang
- Pediatric Intensive Care Unit The First Affiliated Hospital of Zhengzhou University Zhengzhou China
| | - Zhi Xiu Qian
- College of Science Henan University of Technology Zhengzhou China
| | - Jiao Nan Yuan
- College of Science Henan University of Technology Zhengzhou China
| | | | - Guang Fu Ji
- National Key Laboratory of Shock Wave and Detonation Physics, Institute of Fluid Physics Chinese Academy of Engineering Physics Mianyang China
| | - Dong Qing Wei
- College of Science Henan University of Technology Zhengzhou China
- State Key laboratory of Microbial Metabolism, College of Life Science and Biotechnology Shanghai Jiao Tong University Shanghai China
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Nangraj AS, Selvaraj G, Kaliamurthi S, Kaushik AC, Cho WC, Wei DQ. Integrated PPI- and WGCNA-Retrieval of Hub Gene Signatures Shared Between Barrett's Esophagus and Esophageal Adenocarcinoma. Front Pharmacol 2020; 11:881. [PMID: 32903837 PMCID: PMC7438937 DOI: 10.3389/fphar.2020.00881] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 05/28/2020] [Indexed: 02/05/2023] Open
Abstract
Esophageal adenocarcinoma (EAC) is a deadly cancer with high mortality rate, especially in economically advanced countries, while Barrett's esophagus (BE) is reported to be a precursor that strongly increases the risk of EAC. Due to the complexity of these diseases, their molecular mechanisms have not been revealed clearly. This study aims to explore the gene signatures shared between BE and EAC based on integrated network analysis. We obtained EAC- and BE-associated microarray datasets GSE26886, GSE1420, GSE37200, and GSE37203 from the Gene Expression Omnibus and ArrayExpress using systematic meta-analysis. These data were accompanied by clinical data and RNAseq data from The Cancer Genome Atlas (TCGA). Weighted gene co-expression network analysis (WGCNA) and differentially expressed gene (DEG) analysis were conducted to explore the relationship between gene sets and clinical traits as well as to discover the key relationships behind the co-expression modules. A differentially expressed gene-based protein-protein interaction (PPI) complex was used to extract hub genes through Cytoscape plugins. As a result, 403 DEGs were excavated, comprising 236 upregulated and 167 downregulated genes, which are involved in the cell cycle and replication pathways. Forty key genes were identified using modules of MCODE, CytoHubba, and CytoNCA with different algorithms. A dark-gray module with 207 genes was identified which having a high correlation with phenotype (gender) in the WGCNA. Furthermore, five shared hub gene signatures (SHGS), namely, pre-mRNA processing factor 4 (PRPF4), serine and arginine-rich splicing factor 1 (SRSF1), heterogeneous nuclear ribonucleoprotein M (HNRNPM), DExH-Box Helicase 9 (DHX9), and origin recognition complex subunit 2 (ORC2), were identified between BE and EAC. SHGS enrichment denotes that RNA metabolism and splicosomes play a key role in esophageal cancer development and progress. We conclude that the PPI complex and WGCNA co-expression network highlight the importance of phenotypic identifying hub gene signatures for BE and EAC.
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Affiliation(s)
- Asma Sindhoo Nangraj
- The State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Gurudeeban Selvaraj
- Center of Interdisciplinary Sciences-Computational Life Sciences, Henan University of Technology, Zhengzhou, China
- *Correspondence: Gurudeeban Selvaraj, ; Dong Qing Wei,
| | - Satyavani Kaliamurthi
- Center of Interdisciplinary Sciences-Computational Life Sciences, Henan University of Technology, Zhengzhou, China
| | - Aman Chandra Kaushik
- The State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, China
| | - Dong Qing Wei
- The State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Center of Interdisciplinary Sciences-Computational Life Sciences, Henan University of Technology, Zhengzhou, China
- Peng Cheng Laboratory, Shenzhen, China
- *Correspondence: Gurudeeban Selvaraj, ; Dong Qing Wei,
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Khan MT, Kaushik AC, Bhatti AI, Zhang YJ, Zhang S, Wei AJ, Malik SI, Wei DQ. Marine Natural Products and Drug Resistance in Latent Tuberculosis. Mar Drugs 2019; 17:md17100549. [PMID: 31561525 PMCID: PMC6836121 DOI: 10.3390/md17100549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 12/16/2022] Open
Abstract
Pyrazinamide (PZA) is the only drug for the elimination of latent Mycobacterium tuberculosis (MTB) isolates. However, due to the increased number of PZA-resistance, the chances of the success of global TB elimination seems to be more prolonged. Recently, marine natural products (MNPs) as an anti-TB agent have received much attention, where some compounds extracted from marine sponge, Haliclona sp. exhibited strong activity under aerobic and hypoxic conditions. In this study, we screened articles from 1994 to 2019 related to marine natural products (MNPs) active against latent MTB isolates. The literature was also mined for the major regulators to map them in the form of a pathway under the dormant stage. Five compounds were found to be more suitable that may be applied as an alternative to PZA for the better management of resistance under latent stage. However, the mechanism of actions behind these compounds is largely unknown. Here, we also applied synthetic biology to analyze the major regulatory pathway under latent TB that might be used for the screening of selective inhibitors among marine natural products (MNPs). We identified key regulators of MTB under latent TB through extensive literature mining and mapped them in the form of regulatory pathway, where SigH is negatively regulated by RshA. PknB, RshA, SigH, and RNA polymerase (RNA-pol) are the major regulators involved in MTB survival under latent stage. Further studies are needed to screen MNPs active against the main regulators of dormant MTB isolates. To reduce the PZA resistance burden, understanding the regulatory pathways may help in selective targets of MNPs from marine natural sources.
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Affiliation(s)
- Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 44000, Pakistan; (M.T.K.); (S.I.M.)
| | - Aman Chandra Kaushik
- The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Aamer Iqbal Bhatti
- Department of Electrical Engineering, Capital University of Science and Technology, Islamabad 44000, Pakistan;
| | - Yu-Juan Zhang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China;
| | - Shulin Zhang
- Department of Immunology and Microbiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China; (S.Z.)
| | - Amie Jinghua Wei
- Department of Immunology and Microbiology, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China; (S.Z.)
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 44000, Pakistan; (M.T.K.); (S.I.M.)
| | - Dong Qing Wei
- The State Key Laboratory of Microbial Metabolism, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Correspondence: ; Tel.: +86-21-3420-4573
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Wei DQ. [Effect of yiqi-yangyin prescription on bile composition of cholelithiasis patients]. Zhong Xi Yi Jie He Za Zhi 1990; 10:470-2, 452. [PMID: 2208433] [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] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
There were 41 postoperative patients of cholelithiasis with manifestation of Qi-Yin deficiency, had treated with Yiqi Yangyin Prescription. The regimens was 2 weeks as a course, thereafter bile specimens were taken through T tube drainage, and biochemical analysis were performed in order to determine the composition in consequence of the comparison of the treated patients with the control groups. There were 19 patients of bile pigment stone in whom 10 treated with the prescription and 9 were served as control. The results showed that the total bilirubin, unconjugated bilirubin, the concentration of calcium ion and the activity of beta-glucuronidase were markedly decreased as compared to those in the control group (P less than 0.05), the concentration of bile acid markedly increased than that in the control group (P less than 0.05). There were 22 patients of cholesterol stone, 11 treated with the prescription and 11 were served as control group. The results were the same as in bile pigment stone group except decreased in conjugated bilirubin (P less than 0.05), and the unconjugated bilirubin were remained unchanged (P greater than 0.05) as compared to the control group. The ratio of unconjugated bilirubin to total bilirubin and the ratio of bile acid to bilirubin were markedly decreased as compared to those in the control group. The above observation showed promptly that Yiqi-Yangyin Prescription gave a promise influence on lithogenic bile of cholelithiasitic patients, and also investigated the mechanism of the prescription used for deficiency patients with biliary troubles.
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Affiliation(s)
- D Q Wei
- Dept. of Surgery, Affiliated Hospital of Hubei College of TCM, Wuhan
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Wei DQ. [Pharmacological study on the effect of herba Pimpinella thellugiana on the metabolism of animal proteins]. Zhong Yao Tong Bao 1986; 11:53-4. [PMID: 2952360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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13
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Wei DQ. [Clinical experience of percutaneous transhepatic cholangiography and drainage (author's transl)]. Zhonghua Nei Ke Za Zhi 1981; 20:553-5. [PMID: 7333164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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