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Hafeez A, Shabbir M, Khan K, Trembley JH, Badshah Y, Zafar S, Shahid K, Shah H, Ashraf NM, Hamid A, Afsar T, Almajwal A, Marium A, Razak S. Possible prognostic impact of PKCι genetic variants in prostate cancer. Cancer Cell Int 2024; 24:24. [PMID: 38200472 PMCID: PMC10782671 DOI: 10.1186/s12935-023-03182-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Single nucleotide polymorphisms (SNPs) have been linked with prostate cancer (PCa) and have shown potential as prognostic markers for advanced stages. Loss of function mutations in PKCι have been linked with increased risk of malignancy by enhancing tumor cell motility and invasion. We have evaluated the impact of two coding region SNPs on the PKCι gene (PRKCI) and their prognostic potential. METHODS Genotypic association of non-synonymous PKCι SNPs rs1197750201 and rs1199520604 with PCa was determined through tetra-ARMS PCR. PKCι was docked with interacting partner Par-6 to determine the effect of these variants on PKCι binding capabilities. Molecular dynamic simulations of PKCι docked with Par-6 were performed to determine variant effects on PKCι protein interactions. The possible impact of changes in PKCι protein interactions on epithelial cell polarity was hypothesized. RESULTS PKCι rs1199520604 mutant genotype TT showed association with PCa (p = 0.0055), while rs1197750201 mutant genotype AA also showed significant association with PCa (P = 0.0006). The binding interaction of PKCι with Par-6 was altered for both variants, with changes in Van der Waals energy and electrostatic energy of docked structures. CONCLUSION Genotypic analysis of two non-synonymous PKCι variants in association with PCa prognosis was performed. Both variants in the PB1 domain showed potential as a prognostic marker for PCa. In silico analysis of the effect of the variants on PKCι protein interactions indicated they may be involved in PCa progression through aberration of epithelial cell polarity pathways.
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Affiliation(s)
- Amna Hafeez
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan.
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Janeen H Trembley
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Minneapolis VA Health Care System Research Service, Minneapolis, MN, USA
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Sameen Zafar
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Kanza Shahid
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Hania Shah
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Naeem Mahmood Ashraf
- Department of Biochemistry and Biotechnology, University of Gujrat, Hafiz Hayat Campus, Gujrat, 50700, Punjab, Pakistan
| | - Arslan Hamid
- University of Bonn, LIMES Institute (AG-Netea), Carl-Troll-Str. 31, 53115, Bonn, Germany
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Afifa Marium
- Department of Healthcare Biotechnology, Rahman School of Applied Biosciences, National University of Sciences and Technology, Atta-Ur, Islamabad, Pakistan
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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Zafar S, Khan K, Badshah Y, Shahid K, Trembley JH, Hafeez A, Ashraf NM, Arslan H, Shabbir M, Afsar T, Almajwal A, Razak S. Correction: Exploring the prognostic significance of PKCε variants in cervical cancer. BMC Cancer 2023; 23:963. [PMID: 37821893 PMCID: PMC10568823 DOI: 10.1186/s12885-023-11416-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023] Open
Affiliation(s)
- Sameen Zafar
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Kanza Shahid
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Janeen H. Trembley
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN USA
- Minneapolis VA Health Care System Research Service, Minneapolis, MN USA
| | - Amna Hafeez
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Hamid Arslan
- University of Bonn, LIMES Institute (AG-Netea), Carl-Troll-Str. 31, 53115 Bonn, Germany
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
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Zafar S, Khan K, Badshah Y, Shahid K, Trembley JH, Hafeez A, Ashraf NM, Arslan H, Shabbir M, Afsar T, Almajwal A, Razak S. Exploring the prognostic significance of PKCε variants in cervical cancer. BMC Cancer 2023; 23:819. [PMID: 37667176 PMCID: PMC10476323 DOI: 10.1186/s12885-023-11236-z] [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: 06/07/2023] [Accepted: 07/29/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Protein Kinase C-epsilon (PKCε) is a member of the novel subfamily of PKCs (nPKCs) that plays a role in cancer development. Studies have revealed that its elevated expression levels are associated with cervical cancer. Previously, we identified pathogenic variations in its different domains through various bioinformatics tools and molecular dynamic simulation. In the present study, the aim was to find the association of its variants rs1553369874 and rs1345511001 with cervical cancer and to determine the influence of these variants on the protein-protein interactions of PKCε, which can lead towards cancer development and poor survival rates. METHODS The association of the variants with cervical cancer and its clinicopathological features was determined through genotyping analysis. Odds ratio and relative risk along with Fisher exact test were calculated to evaluate variants significance and disease risk. Protein-protein docking was performed and docked complexes were subjected to molecular dynamics simulation to gauge the variants impact on PKCε's molecular interactions. RESULTS This study revealed that genetic variants rs1553369874 and rs1345511001 were associated with cervical cancer. Smad3 interacts with PKCε and this interaction promotes cervical cancer angiogenesis; therefore, Smad3 was selected for protein-protein docking. The analysis revealed PKCε variants promoted aberrant interactions with Smad3 that might lead to the activation of oncogenic pathways. The data obtained from this study suggested the prognostic significance of PRKCE gene variants rs1553369874 and rs1345511001. CONCLUSION Through further in vitro and in vivo validation, these variants can be used at the clinical level as novel prognostic markers and therapeutic targets against cervical cancer.
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Affiliation(s)
- Sameen Zafar
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan.
| | - Kanza Shahid
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Janeen H Trembley
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Minneapolis VA Health Care System Research Service, Minneapolis, MN, USA
| | - Amna Hafeez
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Hamid Arslan
- University of Bonn, LIMES Institute (AG-Netea), Carl-Troll-Str. 31, 53115, Bonn, Germany
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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Shahid K, Khan K, Badshah Y, Mahmood Ashraf N, Hamid A, Trembley JH, Shabbir M, Afsar T, Almajwal A, Abusharha A, Razak S. Pathogenicity of PKCγ Genetic Variants-Possible Function as a Non-Invasive Diagnostic Biomarker in Ovarian Cancer. Genes (Basel) 2023; 14:236. [PMID: 36672978 PMCID: PMC9858858 DOI: 10.3390/genes14010236] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/06/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Ovarian cancer has the highest mortality rate among gynecologic malignancies, owing to its misdiagnosis or late diagnosis. Identification of its genetic determinants could improve disease outcomes. Conventional Protein Kinase C-γ (PKCγ) dysregulation is reported in several cancers. Similarly, its variant rs1331262028 is also reported to have an association with hepatocellular carcinoma. Therefore, the aim of the present study was to analyze the variant rs1331262028 association with ovarian cancer and to determine its impact on PKCγ's protein interactions. Association of variation was determined through genotyping PCR (cohort size:100). Protein-protein docking and molecular dynamic simulation were carried out to study the variant impact of PKCγ interactions. The study outcome indicated the positive association of variant rs1331262028 with ovarian cancer and its clinicopathological features. Molecular dynamics simulation depicted the potential influence of variation on PKCγ molecular signaling. Hence, this study provided the foundations for assessing variant rs1331262028 as a potential prognostic marker for ovarian cancer. Through further validation, it can be applied at the clinical level.
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Affiliation(s)
- Kanza Shahid
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44010, Pakistan
| | - Khushbukhat Khan
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44010, Pakistan
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44010, Pakistan
| | - Naeem Mahmood Ashraf
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore 54590, Pakistan
| | - Arslan Hamid
- LIMES Institute (AG-Netea), University of Bonn, Carl-Troll-Str. 31, 53115 Bonn, Germany
| | - Janeen H. Trembley
- Minneapolis VA Health Care System Research Service, Minneapolis, MN 55417, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Atta-Ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44010, Pakistan
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Ali Abusharha
- Department of Optometry, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi Arabia
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Khan K, Zafar S, Hafeez A, Badshah Y, Shahid K, Mahmood Ashraf N, Shabbir M. PRKCE non-coding variants influence on transcription as well as translation of its gene. RNA Biol 2022; 19:1115-1129. [PMID: 36299231 PMCID: PMC9621080 DOI: 10.1080/15476286.2022.2139110] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 08/15/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 10/31/2022] Open
Abstract
Untranslated regions of the gene play a crucial role in gene expression regulation at mRNA and protein levels. Mutations at UTRs impact expression by altering transcription factor binding, transcriptional/translational efficacy, miRNA-mediated gene regulation, mRNA secondary structure, ribosomal translocation, and stability. PKCε, a serine/threonine kinase, is aberrantly expressed in numerous diseases such as cardiovascular disorders, neurological disorders, and cancers; its probable cause is unknown. Therefore, in the current study, the influence of PRKCE 5'-and 3'UTR variants was explored for their potential impact on its transcription and translation through several bioinformatics approaches. UTR variants data was obtained through different databases and initially evaluated for their regulatory function. Variants with regulatory function were then studied for their effect on PRKCE binding with transcription factors (TF) and miRNAs, as well as their impact on mRNA secondary structure. Study outcomes indicated the regulatory function of 73 5'UTR and 17 3'UTR variants out of 376. 5'UTR variants introduced AP1 binding sites and promoted the PRKCE transcription. Four 3'UTR variants introduced a circular secondary structure, increasing PRKCE translational efficacy. A region in 5'UTR position 45,651,564 to 45,651,644 was found where variants readily influenced the miRNA-PRKCE mRNA binding. The study further highlighted a PKCε-regulated feedback loop mechanism that induces the activity of TFs, promoting its gene transcription. The study provides foundations for experimentation to understand these variants' role in diseases. These variants can also serve as the genetic markers for different diseases' diagnoses after validation at the cell and population levels.
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Affiliation(s)
- Khushbukhat Khan
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Sameen Zafar
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Amna Hafeez
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Yasmin Badshah
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Kanza Shahid
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Naeem Mahmood Ashraf
- School of Biochemistry & Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Maria Shabbir
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
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Shahid K, Shahzadi S, Ali S. Spectroscopic studies of biologically active organotin(IV) derivatives of 2-[N-(2,4,6-tribromophenylamido]propanoic acid. JICS 2008. [DOI: 10.1007/bf03246137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Affiliation(s)
- S. Shahzadi
- a Department of Chemistry , Quaid-i-Azam University , Islamabad, 45320, Pakistan
| | - K. Shahid
- a Department of Chemistry , Quaid-i-Azam University , Islamabad, 45320, Pakistan
| | - S. Ali
- a Department of Chemistry , Quaid-i-Azam University , Islamabad, 45320, Pakistan
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Shahzadi S, Shahid K, Ali S. Coordination behavior of the carboxylate group in organotin(IV) derivatives of 2-[(2′,4′,6′-tribromophenylamido)]benzoic acid and 3-[(2′,4′,6′-tribromophenylamido)]propenoic acid: Spectroscopic studies. RUSS J COORD CHEM+ 2007. [DOI: 10.1134/s1070328407060048] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Shahpurwala MM, Sani N, Shah S, Shuja F, Shahid K, Tariq H, Huda Z, Zuberi L, Jafar TH, Jafar TH. General medical practitioners in Pakistan fail to educate patients adequately about complications of diabetes. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/pdi.897] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Shahzadi S, Shahid K, Ali S, Mazhar M, Khan KM. Organotin(IV) derivatives as biocides: An investigation of structure by IR, solution NMR, electron impact MS and assessment of structure correlation with biocidal activity. JICS 2005. [DOI: 10.1007/bf03245931] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Shahid K, Shahzadi S, Ali S, Bhatti MH, Khan KM. Organotin(IV) complexes of 4-(2,5-dioxo-2,5-dihydro-1H-pyrrol-1-yl)benzoic acid: Synthesis, spectral characterization and biological applications. JICS 2005. [DOI: 10.1007/bf03247205] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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