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Bhattacharjya A, Islam MM, Uddin MA, Talukder MA, Azad A, Aryal S, Paul BK, Tasnim W, Almoyad MAA, Moni MA. Exploring gene regulatory interaction networks and predicting therapeutic molecules for hypopharyngeal cancer and EGFR-mutated lung adenocarcinoma. FEBS Open Bio 2024. [PMID: 38783639 DOI: 10.1002/2211-5463.13807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 01/30/2024] [Accepted: 04/16/2024] [Indexed: 05/25/2024] Open
Abstract
Hypopharyngeal cancer gene regulatory networks and therapeutic molecules are a disease that is associated with EGFR-mutated lung adenocarcinoma. Here we utilized a bioinformatics approach to identify genetic commonalities between these two diseases. To this end, we examined microarray datasets from GEO (Gene Expression Omnibus) to identify differentially expressed genes, common genes, and hub genes between the selected two diseases. Our analyses identified potential therapeutic molecules for the selected diseases based on 10 hub genes with the highest interactions according to the degree topology method and the maximum clique centrality (MCC). These therapeutic molecules may have the potential for simultaneous treatment of these diseases.
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Affiliation(s)
- Abanti Bhattacharjya
- Department of Computer Science and Engineering, Jagannath University, Dhaka, Bangladesh
| | - Md Manowarul Islam
- Department of Computer Science and Engineering, Jagannath University, Dhaka, Bangladesh
| | - Md Ashraf Uddin
- School of Information Technology, Deakin University, Geelong, Australia
| | - Md Alamin Talukder
- Department of Computer Science and Engineering, International University of Business Agriculture and Technology, Dhaka, Bangladesh
| | - Akm Azad
- Department of Mathematics and Statistics, Faculty of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Sunil Aryal
- School of Information Technology, Deakin University, Geelong, Australia
| | - Bikash Kumar Paul
- Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
- Department of Software Engineering, Daffodil International University, Dhaka, Bangladesh
| | - Wahia Tasnim
- Department of Information and Communication Technology, Mawlana Bhashani Science and Technology University, Tangail, Bangladesh
| | | | - Mohammad Ali Moni
- Artificial Intelligence & Data Science, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, Australia
- AI & Digital Health Technology, Artificial Intelligence and Cyber Futures Institute, Charles Sturt University, Bathurst, Australia
- Rural Health Research Institute, Charles Sturt University, Orange, Australia
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Basar MA, Hosen MF, Kumar Paul B, Hasan MR, Shamim S, Bhuyian T. Identification of drug and protein-protein interaction network among stress and depression: A bioinformatics approach. INFORMATICS IN MEDICINE UNLOCKED 2023. [DOI: 10.1016/j.imu.2023.101174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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Khamaru M, Nath D, Mitra D, Roy S. Assessing Combinatorial Diversity of Aureochrome Basic Leucine Zippers through Genome-Wide Screening. Cells Tissues Organs 2022; 213:133-146. [PMID: 36261029 DOI: 10.1159/000527593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022] Open
Abstract
Aureochromes are unique blue light-responsive light-oxygen-voltage (LOV) photoreceptors cum basic leucine zipper (bZIP) transcription factors (TFs), present exclusively in photosynthetic marine stramenopiles. Considering the availability of the complete genome sequence, this study focuses on aureochromes from Ectocarpus siliculosus. Aureochromes mediate light-regulated developmental responses in these brown photosynthetic algae. Both the LOV sensor and the bZIP effector show overall sequence-structure conservation. The structurally similar LOV + bZIP modules of aureochrome homologs/paralogs prefer a dimeric state. Besides a heterogeneous linker connecting the sensor-effector and a flexible N-terminal region, the sequence composition of both domains is vital. Aureochromes execute diverse cellular responses in different photosynthetic stramenopiles - though their activities can vary even within a given algal species. Therefore, it is important to understand whether aureochromes select dimerization partners from the same family or interact with other bZIPs as well. To regulate multifarious biological activities, it is possible that aureochromes activate the global TF interaction network. Following homo/heterodimer modeling, we address the compatibility of dimerization partners by screening through heptad repeats. We evaluate the dimer interface area in terms of gain in solvation energy and the number of hydrogen bonds/salt bridge interactions. We further explore the relative stability of these structures from a graph-theoretic perspective through well-studied measures such as the energy of the graph, average participation coefficient, and betweenness centrality. Furthermore, we also conduct an information-theoretic analysis using hitherto understudied measures such as network information centrality and Kullback-Leibler divergence. We find that all our investigations into the relative stability of the dimers using diverse methods from bioinformatics, network science, and information theory are in harmonious agreement. Coupling preferences of monomers in aureochromes can be further translated to design novel optogenetic tools useful for understanding human development and disease.
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Affiliation(s)
| | - Deep Nath
- Department of Physics, Bose Institute, Kolkata, India
| | - Devrani Mitra
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Soumen Roy
- Department of Physics, Bose Institute, Kolkata, India
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