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  1. Article ; Online: The Role of miRNAs, circRNAs and Their Interactions in Development and Progression of Hepatocellular Carcinoma: An

    Ishaq, Yasmeen / Ikram, Aqsa / Alzahrani, Badr / Khurshid, Sana

    Genes

    2022  Volume 14, Issue 1

    Abstract: Hepatocellular carcinoma (HCC) is a type of malignant tumor. miRNAs are noncoding RNAs and their differential expression patterns are observed in HCC-induced by alcoholism, HBV and HCV infections. By acting as a competing endogenous RNA (ceRNA), circRNA ... ...

    Abstract Hepatocellular carcinoma (HCC) is a type of malignant tumor. miRNAs are noncoding RNAs and their differential expression patterns are observed in HCC-induced by alcoholism, HBV and HCV infections. By acting as a competing endogenous RNA (ceRNA), circRNA regulates the miRNA function, indirectly controlling the gene expression and leading to HCC progression. In the present study, data mining was performed to screen out all miRNAs and circRNA involved in alcohol, HBV or HCV-induced HCC with statistically significant (≤0.05%) expression levels reported in various studies. Further, the interaction of miRNAs and circRNA was also investigated to explore their role in HCC due to various causative agents. Together, these study data provide a deeper understanding of the circRNA-miRNA regulatory mechanisms in HCC. These screened circRNA, miRNA and their interactions can be used as prognostic biomarkers or therapeutic targets for the treatment of HCC.
    MeSH term(s) Humans ; Carcinoma, Hepatocellular/pathology ; MicroRNAs/genetics ; MicroRNAs/metabolism ; RNA, Circular/genetics ; RNA, Circular/metabolism ; Liver Neoplasms/pathology ; Hepatitis C
    Chemical Substances MicroRNAs ; RNA, Circular
    Language English
    Publishing date 2022-12-21
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2527218-4
    ISSN 2073-4425 ; 2073-4425
    ISSN (online) 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14010013
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: The Role of miRNAs, circRNAs and Their Interactions in Development and Progression of Hepatocellular Carcinoma: An Insilico Approach

    Ishaq, Yasmeen / Ikram, Aqsa / Alzahrani, Badr / Khurshid, Sana

    Genes (Basel). 2022 Dec. 21, v. 14, no. 1

    2022  

    Abstract: Hepatocellular carcinoma (HCC) is a type of malignant tumor. miRNAs are noncoding RNAs and their differential expression patterns are observed in HCC-induced by alcoholism, HBV and HCV infections. By acting as a competing endogenous RNA (ceRNA), circRNA ... ...

    Abstract Hepatocellular carcinoma (HCC) is a type of malignant tumor. miRNAs are noncoding RNAs and their differential expression patterns are observed in HCC-induced by alcoholism, HBV and HCV infections. By acting as a competing endogenous RNA (ceRNA), circRNA regulates the miRNA function, indirectly controlling the gene expression and leading to HCC progression. In the present study, data mining was performed to screen out all miRNAs and circRNA involved in alcohol, HBV or HCV-induced HCC with statistically significant (≤0.05%) expression levels reported in various studies. Further, the interaction of miRNAs and circRNA was also investigated to explore their role in HCC due to various causative agents. Together, these study data provide a deeper understanding of the circRNA–miRNA regulatory mechanisms in HCC. These screened circRNA, miRNA and their interactions can be used as prognostic biomarkers or therapeutic targets for the treatment of HCC.
    Keywords alcohol abuse ; alcohols ; biomarkers ; gene expression ; gene expression regulation ; hepatoma ; microRNA ; therapeutics
    Language English
    Dates of publication 2022-1221
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article ; Online
    ZDB-ID 2527218-4
    ISSN 2073-4425
    ISSN 2073-4425
    DOI 10.3390/genes14010013
    Database NAL-Catalogue (AGRICOLA)

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  3. Article: An In Silico Deep Learning Approach to Multi-Epitope Vaccine Design: A Hepatitis E Virus Case Study.

    Ikram, Aqsa / Alzahrani, Badr / Zaheer, Tahreem / Sattar, Sobia / Rasheed, Sidra / Aurangzeb, Muhammad / Ishaq, Yasmeen

    Vaccines

    2023  Volume 11, Issue 3

    Abstract: Hepatitis E Virus (HEV) is a major cause of acute and chronic hepatitis. The severity of HEV infection increases manyfold in pregnant women and immunocompromised patients. Despite the extensive research on HEV in the last few decades, there is no widely ... ...

    Abstract Hepatitis E Virus (HEV) is a major cause of acute and chronic hepatitis. The severity of HEV infection increases manyfold in pregnant women and immunocompromised patients. Despite the extensive research on HEV in the last few decades, there is no widely available vaccine yet. In the current study, immunoinformatic analyses were applied to predict a multi-epitope vaccine candidate against HEV. From the ORF2 region, 41 conserved and immunogenic epitopes were prioritized. These epitopes were further analyzed for their probable antigenic and non-allergenic combinations with several linkers. The stability of the vaccine construct was confirmed by molecular dynamic simulations. The vaccine construct is potentially antigenic and docking analysis revealed stable interactions with TLR3. These results suggest that the proposed vaccine can efficiently stimulate both cellular and humoral immune responses. However, further studies are needed to determine the immunogenicity of the vaccine construct.
    Language English
    Publishing date 2023-03-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines11030710
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article: Assessing the multitargeted antidiabetic potential of three pomegranate peel-specific metabolites: An in silico and pharmacokinetics study.

    Gull, Hina / Ikram, Aqsa / Khalil, Anees Ahmed / Ahmed, Zahoor / Nemat, Arash

    Food science & nutrition

    2023  Volume 11, Issue 11, Page(s) 7188–7205

    Abstract: Diabetes is a chronic metabolic disorder that occurs due to impaired secretion of insulin, insulin resistance, or both. Recent studies show that the antidiabetic drugs used to control hyperglycemic levels are associated with undesirable adverse effects. ... ...

    Abstract Diabetes is a chronic metabolic disorder that occurs due to impaired secretion of insulin, insulin resistance, or both. Recent studies show that the antidiabetic drugs used to control hyperglycemic levels are associated with undesirable adverse effects. Therefore, developing a safe and effective medicine with antidiabetic potential is needed. In this context, in silico studies are considered a rapid, effectual, and cost-effective method in drug discovery procedures. It is evident from the literature that plant-based natural components have shown promising outcomes in drug development to alleviate various diseases and hence have diversified the screening of potential antidiabetic agents. Purposely, in the present study, an in silico approach was performed on three
    Language English
    Publishing date 2023-09-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2703010-6
    ISSN 2048-7177
    ISSN 2048-7177
    DOI 10.1002/fsn3.3644
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Does Cross-neutralization of SARS-CoV-2 Only Relate to High Pathogenic Coronaviruses?

    Ma, Zhongren / Li, Pengfei / Ikram, Aqsa / Pan, Qiuwei

    Trends in immunology

    2020  Volume 41, Issue 10, Page(s) 851–853

    Keywords covid19
    Language English
    Publishing date 2020-08-08
    Publishing country England
    Document type Letter ; Research Support, Non-U.S. Gov't ; Comment
    ZDB-ID 2036831-8
    ISSN 1471-4981 ; 1471-4906
    ISSN (online) 1471-4981
    ISSN 1471-4906
    DOI 10.1016/j.it.2020.08.002
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: The Impact of Mutations on the Pathogenic and Antigenic Activity of SARS-CoV-2 during the First Wave of the COVID-19 Pandemic: A Comprehensive Immunoinformatics Analysis.

    Baloch, Zulqarnain / Ikram, Aqsa / Hakim, Mohamad S / Awan, Faryal Mehwish

    Vaccines

    2021  Volume 9, Issue 12

    Abstract: An in-depth analysis of first-wave SARS-CoV-2 genome is required to identify various mutations that significantly affect viral fitness. In the present study, we performed a comprehensive in silico mutational analysis of 3C-like protease (3CLpro), RNA- ... ...

    Abstract An in-depth analysis of first-wave SARS-CoV-2 genome is required to identify various mutations that significantly affect viral fitness. In the present study, we performed a comprehensive in silico mutational analysis of 3C-like protease (3CLpro), RNA-dependent RNA polymerase (RdRp), and spike (S) proteins with the aim of gaining important insights into first-wave virus mutations and their functional and structural impact on SARS-CoV-2 proteins. Our integrated analysis gathered 6000 SARS-CoV-2 sequences and identified 92 mutations in S, 37 in RdRp, and 11 in 3CLpro regions. The impact of these mutations was also investigated using various in silico approaches. Among these, 32 mutations in S, 15 in RdRp, and 3 in 3CLpro proteins were found to be deleterious in nature and could alter the structural and functional behavior of the encoded proteins. The D614G mutation in spike and the P323Lmutation in RdRp are the globally dominant variants with a high frequency. Most of the identified mutations were also found in the binding moiety of the viral proteins which determine their critical involvement in host-pathogen interactions and may represent drug targets. Furthermore, potential CD4
    Language English
    Publishing date 2021-11-30
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines9121410
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Cross-reactivity towards SARS-CoV-2: the potential role of low-pathogenic human coronaviruses.

    Ma, Zhongren / Li, Pengfei / Ji, Yuepeng / Ikram, Aqsa / Pan, Qiuwei

    The Lancet. Microbe

    2020  Volume 1, Issue 4, Page(s) e151

    MeSH term(s) COVID-19 ; Cross Reactions ; Humans ; SARS-CoV-2
    Language English
    Publishing date 2020-08-06
    Publishing country England
    Document type Letter
    ISSN 2666-5247
    ISSN (online) 2666-5247
    DOI 10.1016/S2666-5247(20)30098-7
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Integrated analysis to study the interplay between post-translational modifications (PTM) in hepatitis C virus proteins and hepatocellular carcinoma (HCC) development.

    Ikram, Aqsa / Rauff, Bisma / Alzahrani, Badr / Awan, Faryal Mehwish / Obaid, Ayesha / Naz, Anam / Kakar, Salik Javed / Janjua, Hussnain Ahmed

    Scientific reports

    2022  Volume 12, Issue 1, Page(s) 15648

    Abstract: Many PTMs dysregulation is known to be the major cause of many cancers including HCV induced HCC. PTMs of hepatitis C virus (HCV) regions NS3/4A, NS5A and NS5B are crucial for proper protein functions and replication that directly affect the generation ... ...

    Abstract Many PTMs dysregulation is known to be the major cause of many cancers including HCV induced HCC. PTMs of hepatitis C virus (HCV) regions NS3/4A, NS5A and NS5B are crucial for proper protein functions and replication that directly affect the generation of infectious virus particles and completion of its life cycle. In this study, we have performed comprehensive analysis of PTMs within HCV non-structural proteins (NS3/4A, NS5A and NS5B) through bioinformatics analysis to examine post-translational crosstalk between phosphorylation, palmitoylation, methylation, acetylation and ubiquitination sites in selected viral proteins. Our analysis has revealed many highly putative PTMs sites that are also conserved among major genotypes conferring the importance of these sites. We have also analysed viral 3D structures in their modified and unmodified forms to address extent and signatures of structural changes upon PTM. This study provides evidence that PTMs induce significant conformational changes and make viral proteins more stable. To find the potential role of PTMs in HCV induced HCC, docking analysis between selected viral proteins and p38-MAPK has been performed which also confirms their strong association with HCV induced HCC. The major findings proposed that PTMs at specific sites of HCV viral proteins could dysregulate specific pathways that cause the development of HCC.
    MeSH term(s) Carcinoma, Hepatocellular ; Hepacivirus/genetics ; Hepatitis C/complications ; Humans ; Liver Neoplasms ; Protein Processing, Post-Translational ; Viral Proteins/genetics
    Chemical Substances Viral Proteins
    Language English
    Publishing date 2022-09-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2615211-3
    ISSN 2045-2322 ; 2045-2322
    ISSN (online) 2045-2322
    ISSN 2045-2322
    DOI 10.1038/s41598-022-19854-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Human Coronavirus Spike Protein Based Multi-Epitope Vaccine against COVID-19 and Potential Future Zoonotic Coronaviruses by Using Immunoinformatic Approaches.

    Baloch, Zulqarnain / Ikram, Aqsa / Shamim, Saba / Obaid, Ayesha / Awan, Faryal Mehwish / Naz, Anam / Rauff, Bisma / Gilani, Khadija / Qureshi, Javed Anver

    Vaccines

    2022  Volume 10, Issue 7

    Abstract: Zoonotic coronaviruses (CoV) have emerged twice and have caused severe respiratory diseases in humans. Due to the frequent outbreaks of different human coronaviruses (HCoVs), the development of a pan-HCoV vaccine is of great importance. Various conserved ...

    Abstract Zoonotic coronaviruses (CoV) have emerged twice and have caused severe respiratory diseases in humans. Due to the frequent outbreaks of different human coronaviruses (HCoVs), the development of a pan-HCoV vaccine is of great importance. Various conserved epitopes shared by HCoVs are reported to induce cross-reactive T-cell responses. Therefore, this study aimed to design a multi-epitope vaccine, targeting the HCoV spike protein. Genetic analysis revealed that the spike region is highly conserved among SARS-CoV-2, bat SL-CoV, and SARS-CoV. By employing the immunoinformatic approach, we prioritized 20 MHC I and 10 MHCII conserved epitopes to design a multi-epitope vaccine. This vaccine candidate is anticipated to strongly elicit both humoral and cell-mediated immune responses. These results warrant further development of this vaccine into real-world application.
    Language English
    Publishing date 2022-07-19
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2703319-3
    ISSN 2076-393X
    ISSN 2076-393X
    DOI 10.3390/vaccines10071150
    Database MEDical Literature Analysis and Retrieval System OnLINE

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