Systems biology approach delineates critical pathways associated with papillary thyroid cancer: a multi-omics data analysis
Abstract Background Papillary thyroid cancer (PTC) is the most prevalent follicular cell-derived subtype of thyroid cancer. A systems biology approach to PTC can elucidate the mechanism by which molecular components work and interact with one another to decipher a panoramic view of the pathophysiolo...
Saved in:
| Main Authors: | , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-04-01
|
| Series: | Thyroid Research |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13044-025-00230-1 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850145675070668800 |
|---|---|
| author | Febby Payva Santhy K. S. Remya James Amrisa Pavithra E Venketesh Sivaramakrishnan |
| author_facet | Febby Payva Santhy K. S. Remya James Amrisa Pavithra E Venketesh Sivaramakrishnan |
| author_sort | Febby Payva |
| collection | DOAJ |
| description | Abstract Background Papillary thyroid cancer (PTC) is the most prevalent follicular cell-derived subtype of thyroid cancer. A systems biology approach to PTC can elucidate the mechanism by which molecular components work and interact with one another to decipher a panoramic view of the pathophysiology. Methodology PTC associated genes and transcriptomic data were retrieved from DisGeNET and Gene Expression Omnibus database respectively. Published proteomic and metabolomic datasets in PTC from EMBL-EBI were used. Gene Ontology and pathway analyses were performed with SNPs, differentially expressed genes (DEGs), proteins, and metabolites linked to PTC. The effect of a nucleotide substitution on a protein's function was investigated. Additionally, significant transcription factors (TFs) and kinases were identified. An integrated strategy was used to analyse the multi-omics data to determine the key deregulated pathways in PTC carcinogenesis. Results Pathways linked to carbohydrate, protein, and lipid metabolism, along with the immune response, signaling, apoptosis, gene expression, epithelial–mesenchymal transition (EMT), and disease onset, were identified as significant for the clinical and functional aspects of PTC. Glyoxylate and dicarboxylate metabolism and citrate cycle were the most common pathways among the PTC omics datasets. Commonality analysis deciphered five TFs and fifty-seven kinases crucial for PTC genesis and progression. Core deregulated pathways, TFs, and kinases modulate critical biological processes like proliferation, angiogenesis, immune infiltration, invasion, autophagy, EMT, and metastasis in PTC. Conclusion Identified dysregulated pathways, TFs and kinases are critical in PTC and may help in systems level understanding and device specific experiments, biomarkers, and drug targets for better management of PTC. |
| format | Article |
| id | doaj-art-960605869503456280e140ffda82a6f6 |
| institution | OA Journals |
| issn | 1756-6614 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Thyroid Research |
| spelling | doaj-art-960605869503456280e140ffda82a6f62025-08-20T02:28:02ZengBMCThyroid Research1756-66142025-04-0118111710.1186/s13044-025-00230-1Systems biology approach delineates critical pathways associated with papillary thyroid cancer: a multi-omics data analysisFebby Payva0Santhy K. S.1Remya James2Amrisa Pavithra E3Venketesh Sivaramakrishnan4Department of Zoology, St. Joseph’s College for WomenDepartment of Zoology, Avinashilingam Institute for Home Science and Higher Education for WomenDepartment of Zoology, St. Joseph’s College for WomenDepartment of Zoology, Avinashilingam Institute for Home Science and Higher Education for WomenDisease Biology Lab, Department of Biosciences, Sri Sathya Sai Institute of Higher LearningAbstract Background Papillary thyroid cancer (PTC) is the most prevalent follicular cell-derived subtype of thyroid cancer. A systems biology approach to PTC can elucidate the mechanism by which molecular components work and interact with one another to decipher a panoramic view of the pathophysiology. Methodology PTC associated genes and transcriptomic data were retrieved from DisGeNET and Gene Expression Omnibus database respectively. Published proteomic and metabolomic datasets in PTC from EMBL-EBI were used. Gene Ontology and pathway analyses were performed with SNPs, differentially expressed genes (DEGs), proteins, and metabolites linked to PTC. The effect of a nucleotide substitution on a protein's function was investigated. Additionally, significant transcription factors (TFs) and kinases were identified. An integrated strategy was used to analyse the multi-omics data to determine the key deregulated pathways in PTC carcinogenesis. Results Pathways linked to carbohydrate, protein, and lipid metabolism, along with the immune response, signaling, apoptosis, gene expression, epithelial–mesenchymal transition (EMT), and disease onset, were identified as significant for the clinical and functional aspects of PTC. Glyoxylate and dicarboxylate metabolism and citrate cycle were the most common pathways among the PTC omics datasets. Commonality analysis deciphered five TFs and fifty-seven kinases crucial for PTC genesis and progression. Core deregulated pathways, TFs, and kinases modulate critical biological processes like proliferation, angiogenesis, immune infiltration, invasion, autophagy, EMT, and metastasis in PTC. Conclusion Identified dysregulated pathways, TFs and kinases are critical in PTC and may help in systems level understanding and device specific experiments, biomarkers, and drug targets for better management of PTC.https://doi.org/10.1186/s13044-025-00230-1Papillary thyroid cancerSystems biologyMulti-omicsDEGsTranscription factorsKinases |
| spellingShingle | Febby Payva Santhy K. S. Remya James Amrisa Pavithra E Venketesh Sivaramakrishnan Systems biology approach delineates critical pathways associated with papillary thyroid cancer: a multi-omics data analysis Thyroid Research Papillary thyroid cancer Systems biology Multi-omics DEGs Transcription factors Kinases |
| title | Systems biology approach delineates critical pathways associated with papillary thyroid cancer: a multi-omics data analysis |
| title_full | Systems biology approach delineates critical pathways associated with papillary thyroid cancer: a multi-omics data analysis |
| title_fullStr | Systems biology approach delineates critical pathways associated with papillary thyroid cancer: a multi-omics data analysis |
| title_full_unstemmed | Systems biology approach delineates critical pathways associated with papillary thyroid cancer: a multi-omics data analysis |
| title_short | Systems biology approach delineates critical pathways associated with papillary thyroid cancer: a multi-omics data analysis |
| title_sort | systems biology approach delineates critical pathways associated with papillary thyroid cancer a multi omics data analysis |
| topic | Papillary thyroid cancer Systems biology Multi-omics DEGs Transcription factors Kinases |
| url | https://doi.org/10.1186/s13044-025-00230-1 |
| work_keys_str_mv | AT febbypayva systemsbiologyapproachdelineatescriticalpathwaysassociatedwithpapillarythyroidcanceramultiomicsdataanalysis AT santhyks systemsbiologyapproachdelineatescriticalpathwaysassociatedwithpapillarythyroidcanceramultiomicsdataanalysis AT remyajames systemsbiologyapproachdelineatescriticalpathwaysassociatedwithpapillarythyroidcanceramultiomicsdataanalysis AT amrisapavithrae systemsbiologyapproachdelineatescriticalpathwaysassociatedwithpapillarythyroidcanceramultiomicsdataanalysis AT venketeshsivaramakrishnan systemsbiologyapproachdelineatescriticalpathwaysassociatedwithpapillarythyroidcanceramultiomicsdataanalysis |