1
|
Hu X, Zhang P, Zhang J, Deng L. DeepFusionCDR: Employing Multi-Omics Integration and Molecule-Specific Transformers for Enhanced Prediction of Cancer Drug Responses. IEEE J Biomed Health Inform 2024; 28:6248-6258. [PMID: 38935469 DOI: 10.1109/jbhi.2024.3417014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Deep learning approaches have demonstrated remarkable potential in predicting cancer drug responses (CDRs), using cell line and drug features. However, existing methods predominantly rely on single-omics data of cell lines, potentially overlooking the complex biological mechanisms governing cell line responses. This paper introduces DeepFusionCDR, a novel approach employing unsupervised contrastive learning to amalgamate multi-omics features, including mutation, transcriptome, methylome, and copy number variation data, from cell lines. Furthermore, we incorporate molecular SMILES-specific transformers to derive drug features from their chemical structures. The unified multi-omics and drug signatures are combined, and a multi-layer perceptron (MLP) is applied to predict IC50 values for cell line-drug pairs. Moreover, this MLP can discern whether a cell line is resistant or sensitive to a particular drug. We assessed DeepFusionCDR's performance on the GDSC dataset and juxtaposed it against cutting-edge methods, demonstrating its superior performance in regression and classification tasks. We also conducted ablation studies and case analyses to exhibit the effectiveness and versatility of our proposed approach. Our results underscore the potential of DeepFusionCDR to enhance CDR predictions by harnessing the power of multi-omics fusion and molecular-specific transformers. The prediction of DeepFusionCDR on TCGA patient data and case study highlight the practical application scenarios of DeepFusionCDR in real-world environments.
Collapse
|
2
|
Zohar Y, Mabjeesh NJ. Targeting HIF-1 for prostate cancer: a synthesis of preclinical evidence. Expert Opin Ther Targets 2023; 27:715-731. [PMID: 37596912 DOI: 10.1080/14728222.2023.2248381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 07/20/2023] [Accepted: 08/10/2023] [Indexed: 08/21/2023]
Abstract
INTRODUCTION Hypoxia-inducible factor (HIF) mediates multiple intracellular processes that drive cellular metabolism and induce proliferation. Dysregulated HIF expression is associated with oncogenic cellular transformation. Moreover, high HIF levels correlate with tumor aggressiveness and chemoresistance, indicating the vital effect of HIF-1α on tumorigenicity. Currently, widespread in-vitro and in-vivo research is focusing on targeting HIF with drugs that have already been approved for use by the FDA, such as belzutifan, in renal cell carcinoma. HIF inhibition is mostly associated with tumor size reduction; however, drug toxicity remains a challenge. AREA COVERED In this review, we focus on the potential of targeting HIF in prostate cancer (PC) and summarize the scientific background of HIF activity in PC. This finding emphasizes the rationale for using HIF as a therapeutic target in this malignancy. We have listed known HIF inhibitors that are being investigated in preclinical studies and their potential as anticancer drugs for PC. EXPERT OPINION Although HIF-targeting agents have been investigated for over a decade, their use in therapy-resistant cancers remains relevant and should be explored further. In addition, the use of naturally occurring HIF inhibitors should be considered as an add-on therapy for the currently used regimens.
Collapse
Affiliation(s)
- Yarden Zohar
- Department of Urology, Health Sciences, Soroka University Medical Center, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| | - Nicola J Mabjeesh
- Department of Urology, Health Sciences, Soroka University Medical Center, Ben-Gurion University of the Negev, Be'er-Sheva, Israel
| |
Collapse
|
3
|
Zhang L, Wu M, Su R, Zhang D, Yang G. The efficacy and mechanism of proteasome inhibitors in solid tumor treatment. Recent Pat Anticancer Drug Discov 2021; 17:268-283. [PMID: 34856915 DOI: 10.2174/1574892816666211202154536] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/06/2021] [Accepted: 11/11/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The ubiquitin-proteasome system (UPS) is critical in cellular protein degradation and widely involved in the regulations of cancer hallmarks. Targeting the UPS pathway has emerged as a promising novel treatment in hematological malignancies and solid tumors. OBJECTIVE This review mainly focuses on the preclinical results of proteasome inhibitors in solid tumors. METHODS We analyzed the published articles associated with the anticancer results of proteasome inhibitors alone or combination chemotherapy in solid tumors. Important data presented in abstract form were also discussed in this review. RESULTS/CONCLUSION Proteasome inhibitors, such as bortezomib and carfilzomib, are highly effective in treating solid tumors. The anticancer efficacy is not limited to affect the proteasomal inhibition-associated signaling pathways but also widely involves the signaling pathways related to cell cycle, apoptosis, and epithelial-mesenchymal transition (EMT). In addition, proteasome inhibitors overcome the conventional chemo-resistance of standard chemotherapeutics by inhibiting signaling pathways, such as NF-κB or PI3K/Akt. Combination chemotherapy of proteasome inhibitors and standard chemotherapeutics are widely investigated in multiple relapsed or chemo-resistant solid tumor types, such as breast cancer and pancreatic cancer. The proteasome inhibitors re-sensitize the standard chemotherapeutic regimens and induce synergistic anticancer effects. The development of novel proteasome inhibitors and delivery systems also improves the proteasome inhibitors' anticancer efficacy in solid tumors. This review summarizes the current preclinical results of proteasome inhibitors in solid tumors and reveals the potential anticancer mechanisms.
Collapse
Affiliation(s)
- Lei Zhang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, 130118. China
| | - Mengyang Wu
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, 130118. China
| | - Ruicong Su
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, 130118. China
| | - Di Zhang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, 130118. China
| | - Guilian Yang
- College of Veterinary Medicine, Jilin Agricultural University, Changchun, 130118. China
| |
Collapse
|
4
|
Zhang Y, Liu Q, Wei W, Zhang G, Yan S, Dai R, Sun Y, Su D, Lv S, Xia Y, Li J, Li C. Bortezomib potentiates antitumor activity of mitoxantrone through dampening Wnt/β-catenin signal pathway in prostate cancer cells. BMC Cancer 2021; 21:1101. [PMID: 34645397 PMCID: PMC8515742 DOI: 10.1186/s12885-021-08841-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 10/05/2021] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Bortezomib (BZM), alone or in combination with other chemotherapies, has displayed strong anticancer effects in several cancers. The efficacy of the combination of BZM and mitoxantrone (MTX) in treating prostate cancer remains unknown. METHODS Anticancer effects of combination of BZM and MTX were determined by apoptosis and proliferation assay in vivo and in vitro. Expression of β-Catenin and its target genes were characterized by western blot and Real-time PCR. RESULTS BZM significantly enhanced MTX-induced antiproliferation in vivo and in vitro. Mice administered a combination of BZM and MTX displayed attenuated tumor growth and prolonged survival. BZM significantly attenuated MTX-induced apoptosis. Moreover, the combination of BZM and MTX contributed to inhibition of the Wnt/β-Catenin signaling pathway compared to monotherapy. CONCLUSIONS This study demonstrates that BZM enhances MTX-induced anti-tumor effects by inhibiting the Wnt/β-Catenin signaling pathway in prostate cancer cells.
Collapse
Affiliation(s)
- Ying Zhang
- Institute of Precision Medicine, Jining Medical University, Jining, 272067, China
| | - Qiuzi Liu
- Institute of Precision Medicine, Jining Medical University, Jining, 272067, China
| | - Wei Wei
- Center for Experimental Medicine, School of Public Health, Jining Medical University, Jining, 272067, China
| | - Guoan Zhang
- Institute of Cancer Pathology Research, Jining Medical University, Jining, 272067, China
| | - Siyuan Yan
- Institute of Precision Medicine, Jining Medical University, Jining, 272067, China
| | - Rongrong Dai
- Institute of Precision Medicine, Jining Medical University, Jining, 272067, China
| | - Ying Sun
- Institute of Precision Medicine, Jining Medical University, Jining, 272067, China
| | - Dubo Su
- Institute of Precision Medicine, Jining Medical University, Jining, 272067, China
| | - Shun Lv
- Laboratory animal center, Jining Medical University, Jining, 272067, China
| | - Yong Xia
- Institute of Precision Medicine, Jining Medical University, Jining, 272067, China
| | - Jing Li
- Department of Histology and Embryology, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Changlin Li
- Institute of Precision Medicine, Jining Medical University, Jining, 272067, China.
| |
Collapse
|