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Jose A, Kulkarni P, Thilakan J, Munisamy M, Malhotra AG, Singh J, Kumar A, Rangnekar VM, Arya N, Rao M. Integration of pan-omics technologies and three-dimensional in vitro tumor models: an approach toward drug discovery and precision medicine. Mol Cancer 2024; 23:50. [PMID: 38461268 PMCID: PMC10924370 DOI: 10.1186/s12943-023-01916-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/15/2023] [Indexed: 03/11/2024] Open
Abstract
Despite advancements in treatment protocols, cancer is one of the leading cause of deaths worldwide. Therefore, there is a need to identify newer and personalized therapeutic targets along with screening technologies to combat cancer. With the advent of pan-omics technologies, such as genomics, transcriptomics, proteomics, metabolomics, and lipidomics, the scientific community has witnessed an improved molecular and metabolomic understanding of various diseases, including cancer. In addition, three-dimensional (3-D) disease models have been efficiently utilized for understanding disease pathophysiology and as screening tools in drug discovery. An integrated approach utilizing pan-omics technologies and 3-D in vitro tumor models has led to improved understanding of the intricate network encompassing various signalling pathways and molecular cross-talk in solid tumors. In the present review, we underscore the current trends in omics technologies and highlight their role in understanding genotypic-phenotypic co-relation in cancer with respect to 3-D in vitro tumor models. We further discuss the challenges associated with omics technologies and provide our outlook on the future applications of these technologies in drug discovery and precision medicine for improved management of cancer.
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Affiliation(s)
- Anmi Jose
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Pallavi Kulkarni
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Jaya Thilakan
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Murali Munisamy
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Anvita Gupta Malhotra
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Jitendra Singh
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Ashok Kumar
- Department of Biochemistry, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India
| | - Vivek M Rangnekar
- Markey Cancer Center and Department of Radiation Medicine, University of Kentucky, Lexington, KY, 40536, USA
| | - Neha Arya
- Department of Translational Medicine, All India Institute of Medical Sciences Bhopal, Bhopal, Madhya Pradesh, 462020, India.
| | - Mahadev Rao
- Department of Pharmacy Practice, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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Breast Cancer: From Pathophysiology to Novel Therapeutic Approaches 2.0. Int J Mol Sci 2023; 24:ijms24032542. [PMID: 36768866 PMCID: PMC9916418 DOI: 10.3390/ijms24032542] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 12/23/2022] [Accepted: 01/13/2023] [Indexed: 01/31/2023] Open
Abstract
Breast cancer (BC) is the most common malignancy in women worldwide [...].
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Neary B, Lin S, Qiu P. Methylation of CpG Sites as Biomarkers Predictive of Drug-Specific
Patient Survival in Cancer. Cancer Inform 2022; 21:11769351221131124. [PMID: 36340286 PMCID: PMC9634212 DOI: 10.1177/11769351221131124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 09/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background: Though the development of targeted cancer drugs continues to accelerate,
doctors still lack reliable methods for predicting patient response to
standard-of-care therapies for most cancers. DNA methylation has been
implicated in tumor drug response and is a promising source of predictive
biomarkers of drug efficacy, yet the relationship between drug efficacy and
DNA methylation remains largely unexplored. Method: In this analysis, we performed log-rank survival analyses on patients grouped
by cancer and drug exposure to find CpG sites where binary methylation
status is associated with differential survival in patients treated with a
specific drug but not in patients with the same cancer who were not exposed
to that drug. We also clustered these drug-specific CpG sites based on
co-methylation among patients to identify broader methylation patterns that
may be related to drug efficacy, which we investigated for transcription
factor binding site enrichment using gene set enrichment analysis. Results: We identified CpG sites that were drug-specific predictors of survival in 38
cancer-drug patient groups across 15 cancers and 20 drugs. These included 11
CpG sites with similar drug-specific survival effects in multiple cancers.
We also identified 76 clusters of CpG sites with stronger associations with
patient drug response, many of which contained CpG sites in gene promoters
containing transcription factor binding sites. Conclusion: These findings are promising biomarkers of drug response for a variety of
drugs and contribute to our understanding of drug-methylation interactions
in cancer. Investigation and validation of these results could lead to the
development of targeted co-therapies aimed at manipulating methylation in
order to improve efficacy of commonly used therapies and could improve
patient survival and quality of life by furthering the effort toward drug
response prediction.
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Affiliation(s)
- Bridget Neary
- School of Biological Sciences, Georgia
Institute of Technology, Atlanta, GA, USA
| | - Shuting Lin
- School of Biological Sciences, Georgia
Institute of Technology, Atlanta, GA, USA
| | - Peng Qiu
- Department of Biomedical Engineering,
Georgia Institute of Technology and Emory University, Atlanta, GA, USA,Peng Qiu, Department of Biomedical
Engineering, Georgia Institute of Technology and Emory University, 950 Atlantic
Dr. NW, Atlanta, GA 30332 USA.
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