BMC3PM: bioinformatics multidrug combination protocol for personalized precision medicine and its application in cancer treatment
Abstract Background In recent years, drug screening has been one of the most significant challenges in the field of personalized medicine, particularly in cancer treatment. However, several new platforms have been introduced to address this issue, providing reliable solutions for personalized drug v...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2023-12-01
|
| Series: | BMC Medical Genomics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12920-023-01745-y |
| _version_ | 1797362816806551552 |
|---|---|
| author | Majid Mokhtari Samane Khoshbakht Mohammad Esmaeil Akbari Sayyed Sajjad Moravveji |
| author_facet | Majid Mokhtari Samane Khoshbakht Mohammad Esmaeil Akbari Sayyed Sajjad Moravveji |
| author_sort | Majid Mokhtari |
| collection | DOAJ |
| description | Abstract Background In recent years, drug screening has been one of the most significant challenges in the field of personalized medicine, particularly in cancer treatment. However, several new platforms have been introduced to address this issue, providing reliable solutions for personalized drug validation and safety testing. In this study, we developed a personalized drug combination protocol as the primary input to such platforms. Methods To achieve this, we utilized data from whole-genome expression profiles of 6173 breast cancer patients, 312 healthy individuals, and 691 drugs. Our approach involved developing an individual pattern of perturbed gene expression (IPPGE) for each patient, which was used as the basis for drug selection. An algorithm was designed to extract personalized drug combinations by comparing the IPPGE and drug signatures. Additionally, we employed the concept of drug repurposing, searching for new benefits of existing drugs that may regulate the desired genes. Results Our study revealed that drug combinations obtained from both specialized and non-specialized cancer medicines were more effective than those extracted from only specialized medicines. Furthermore, we observed that the individual pattern of perturbed gene expression (IPPGE) was unique to each patient, akin to a fingerprint. Conclusions The personalized drug combination protocol developed in this study offers a methodological interface between drug repurposing and combination drug therapy in cancer treatment. This protocol enables personalized drug combinations to be extracted from hundreds of drugs and thousands of drug combinations, potentially offering more effective treatment options for cancer patients. |
| first_indexed | 2024-03-08T16:12:51Z |
| format | Article |
| id | doaj.art-eb1cdeb0ba3a486ba4374818d420000e |
| institution | Directory Open Access Journal |
| issn | 1755-8794 |
| language | English |
| last_indexed | 2024-03-08T16:12:51Z |
| publishDate | 2023-12-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Medical Genomics |
| spelling | doaj.art-eb1cdeb0ba3a486ba4374818d420000e2024-01-07T12:52:51ZengBMCBMC Medical Genomics1755-87942023-12-0116111510.1186/s12920-023-01745-yBMC3PM: bioinformatics multidrug combination protocol for personalized precision medicine and its application in cancer treatmentMajid Mokhtari0Samane Khoshbakht1Mohammad Esmaeil Akbari2Sayyed Sajjad Moravveji3Department of Bioinformatics, Kish International Campus, University of TehranDepartment of Bioinformatics, Kish International Campus, University of TehranCancer Research Center, Shahid Beheshti University of Medical SciencesDepartment of Bioinformatics, Kish International Campus, University of TehranAbstract Background In recent years, drug screening has been one of the most significant challenges in the field of personalized medicine, particularly in cancer treatment. However, several new platforms have been introduced to address this issue, providing reliable solutions for personalized drug validation and safety testing. In this study, we developed a personalized drug combination protocol as the primary input to such platforms. Methods To achieve this, we utilized data from whole-genome expression profiles of 6173 breast cancer patients, 312 healthy individuals, and 691 drugs. Our approach involved developing an individual pattern of perturbed gene expression (IPPGE) for each patient, which was used as the basis for drug selection. An algorithm was designed to extract personalized drug combinations by comparing the IPPGE and drug signatures. Additionally, we employed the concept of drug repurposing, searching for new benefits of existing drugs that may regulate the desired genes. Results Our study revealed that drug combinations obtained from both specialized and non-specialized cancer medicines were more effective than those extracted from only specialized medicines. Furthermore, we observed that the individual pattern of perturbed gene expression (IPPGE) was unique to each patient, akin to a fingerprint. Conclusions The personalized drug combination protocol developed in this study offers a methodological interface between drug repurposing and combination drug therapy in cancer treatment. This protocol enables personalized drug combinations to be extracted from hundreds of drugs and thousands of drug combinations, potentially offering more effective treatment options for cancer patients.https://doi.org/10.1186/s12920-023-01745-yDrug repurposingGene expressionBreast cancerMicroarrayOncology |
| spellingShingle | Majid Mokhtari Samane Khoshbakht Mohammad Esmaeil Akbari Sayyed Sajjad Moravveji BMC3PM: bioinformatics multidrug combination protocol for personalized precision medicine and its application in cancer treatment BMC Medical Genomics Drug repurposing Gene expression Breast cancer Microarray Oncology |
| title | BMC3PM: bioinformatics multidrug combination protocol for personalized precision medicine and its application in cancer treatment |
| title_full | BMC3PM: bioinformatics multidrug combination protocol for personalized precision medicine and its application in cancer treatment |
| title_fullStr | BMC3PM: bioinformatics multidrug combination protocol for personalized precision medicine and its application in cancer treatment |
| title_full_unstemmed | BMC3PM: bioinformatics multidrug combination protocol for personalized precision medicine and its application in cancer treatment |
| title_short | BMC3PM: bioinformatics multidrug combination protocol for personalized precision medicine and its application in cancer treatment |
| title_sort | bmc3pm bioinformatics multidrug combination protocol for personalized precision medicine and its application in cancer treatment |
| topic | Drug repurposing Gene expression Breast cancer Microarray Oncology |
| url | https://doi.org/10.1186/s12920-023-01745-y |
| work_keys_str_mv | AT majidmokhtari bmc3pmbioinformaticsmultidrugcombinationprotocolforpersonalizedprecisionmedicineanditsapplicationincancertreatment AT samanekhoshbakht bmc3pmbioinformaticsmultidrugcombinationprotocolforpersonalizedprecisionmedicineanditsapplicationincancertreatment AT mohammadesmaeilakbari bmc3pmbioinformaticsmultidrugcombinationprotocolforpersonalizedprecisionmedicineanditsapplicationincancertreatment AT sayyedsajjadmoravveji bmc3pmbioinformaticsmultidrugcombinationprotocolforpersonalizedprecisionmedicineanditsapplicationincancertreatment |