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Ding Y, Bajpai AK, Wu F, Lu W, Xu L, Mao J, Li Q, Pan Q, Lu L, Wang X. 5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia. Aging (Albany NY) 2024; 16:2340-2361. [PMID: 38277218 PMCID: PMC10911375 DOI: 10.18632/aging.205484] [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: 09/22/2023] [Accepted: 12/26/2023] [Indexed: 01/27/2024]
Abstract
Acute myeloid leukemia (AML) is a highly heterogeneous malignant disease of the blood cell. The current therapies for AML are unsatisfactory and the molecular mechanisms underlying AML are unclear. 5-methylcytosine (m5C) is an important posttranscriptional modification of mRNA, and is involved in the regulation of mRNA stability, translation, and other aspects of RNA metabolism. However, based on our knowledge of published literature, the role of the m5C regulators has not been explored in AML till date. In this study, we clarified the expression and gene variants of m5C regulators in AML and found that most m5C regulators were differentially expressed and correlated with disease prognosis. We also found that the methylation status of certain m5C regulators (e.g., DNMT3A, DNMT3B) affects the survival of AML patients. Two m5C modification subtypes, and high- and low-risk subgroups identified based on the expression of m5C regulators showed significant differences in the prognosis as well as immune cell infiltration. In addition, most of the m5C regulators were found to be correlated with miRNA expression in AML, as well as IC50 values of many drugs. The miRNA and GSVA analysis were used to identify the different miRNAs and KEGG or hallmark pathways between high- and low-risk subgroups. We also built a prognostic model based on m5C regulators, which was validated by two GSE databases. To verify the reliability of our analysis and conclusions, qPCR was used to identify the expressions of m5C regulators between normal and AML. In summary, we comprehensively explored the molecular characteristics of m5C regulators and built a prognostic model in AML. We proposed new mechanistic insights into the role of m5C in multiple databases and clinical data, which may pave novel ways for the development of therapeutic strategies.
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Affiliation(s)
- Yuhong Ding
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Akhilesh K. Bajpai
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Cente, Memphis, TN 38163, USA
| | - Fengxia Wu
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Weihua Lu
- Department of Hematology and Oncology, The Branch Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Lin Xu
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Jiawei Mao
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Qiang Li
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Qi Pan
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
| | - Lu Lu
- Department of Genetics, Genomics and Informatics University of Tennessee Health Science Cente, Memphis, TN 38163, USA
| | - Xinfeng Wang
- Department of Hematology, The Affiliated Hospital of Nantong University, Jiangsu 226000, China
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Vancoppenolle JM, Koole SN, O'Mahony JF, Franzen N, Burgers JA, Retèl VP, van Harten WH. Targeted combination therapies in oncology: challenging regulatory frameworks designed for monotherapies in Europe. Drug Discov Today 2023:103620. [PMID: 37201780 DOI: 10.1016/j.drudis.2023.103620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/08/2023] [Accepted: 05/11/2023] [Indexed: 05/20/2023]
Abstract
The pharmaceutical value chain, including clinical trials, pricing, access, and reimbursement, is designed for classical monotherapies. Although there has been a paradigm shift that increases the relevance of targeted combination therapies (TCTs), regulation and common practice have been slow to adapt. We explored access to 23 TCTs for advanced melanoma and lung cancer as reported by 19 specialists from 17 leading cancer institutions in nine European countries. We find heterogeneous patient access to TCTs between countries, differences in country-specific regulations, and differences in the clinical practice of melanoma and lung cancer. Regulation that is better tailored to the context of combinational therapies can increase equity in access across Europe and promote an evidence-based and authorized use of combinations.
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Affiliation(s)
- Julie M Vancoppenolle
- The European Fain Pricing Network, Amsterdam, The Netherlands; Netherlands Cancer Institute-Antoni van Leeuwenhoek Amsterdam, The Netherlands; Health Technology and Services Research Department, Technical Medical Centre, University of Twente, Enschede, The Netherlands
| | - Simone N Koole
- The European Fain Pricing Network, Amsterdam, The Netherlands; Netherlands Cancer Institute-Antoni van Leeuwenhoek Amsterdam, The Netherlands
| | - James F O'Mahony
- Organization of European Cancer Institutes (OECI), Brussels B 1000, Belgium; Centre for Health Policy and Management, School of Medicine, Trinity College Dublin, Dublin, Ireland
| | - Nora Franzen
- The European Fain Pricing Network, Amsterdam, The Netherlands; Netherlands Cancer Institute-Antoni van Leeuwenhoek Amsterdam, The Netherlands; Health Technology and Services Research Department, Technical Medical Centre, University of Twente, Enschede, The Netherlands
| | - Jacobus A Burgers
- Netherlands Cancer Institute-Antoni van Leeuwenhoek Amsterdam, The Netherlands
| | - Valesca P Retèl
- Netherlands Cancer Institute-Antoni van Leeuwenhoek Amsterdam, The Netherlands; Health Technology and Services Research Department, Technical Medical Centre, University of Twente, Enschede, The Netherlands
| | - Willem H van Harten
- The European Fain Pricing Network, Amsterdam, The Netherlands; Netherlands Cancer Institute-Antoni van Leeuwenhoek Amsterdam, The Netherlands; Health Technology and Services Research Department, Technical Medical Centre, University of Twente, Enschede, The Netherlands; Organization of European Cancer Institutes (OECI), Brussels B 1000, Belgium.
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Babaei M, Evers TMJ, Shokri F, Altucci L, de Lange ECM, Mashaghi A. Biochemical reaction network topology defines dose-dependent Drug-Drug interactions. Comput Biol Med 2023; 155:106584. [PMID: 36805215 DOI: 10.1016/j.compbiomed.2023.106584] [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: 09/20/2022] [Revised: 12/28/2022] [Accepted: 01/22/2023] [Indexed: 01/29/2023]
Abstract
Drug combination therapy is a promising strategy to enhance the desired therapeutic effect, while reducing side effects. High-throughput pairwise drug combination screening is a commonly used method for discovering favorable drug interactions, but is time-consuming and costly. Here, we investigate the use of reaction network topology-guided design of combination therapy as a predictive in silico drug-drug interaction screening approach. We focused on three-node enzymatic networks, with general Michaelis-Menten kinetics. The results revealed that drug-drug interactions critically depend on the choice of target arrangement in a given topology, the nature of the drug, and the desired level of change in the network output. The results showed a negative correlation between antagonistic interactions and the dosage of drugs. Overall, the negative feedback loops showed the highest synergistic interactions (the lowest average combination index) and, intriguingly, required the highest drug doses compared to other topologies under the same condition.
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Affiliation(s)
- Mehrad Babaei
- Medical Systems Biophysics and Bioengineering, Systems Pharmacology and Pharmacy Division, Leiden Academic Centre for Drug Research, Leiden University, Leiden, 2333CC, the Netherlands; Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy.
| | - Tom M J Evers
- Medical Systems Biophysics and Bioengineering, Systems Pharmacology and Pharmacy Division, Leiden Academic Centre for Drug Research, Leiden University, Leiden, 2333CC, the Netherlands.
| | - Fereshteh Shokri
- Leiden University Medical Center, Leiden, 2333ZA, the Netherlands.
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy; BIOGEM, Molecular Biology and Genetics Research Institute, Ariano Irpino, Italy.
| | - Elizabeth C M de Lange
- Predictive Pharmacology, Systems Pharmacology and Pharmacy Division, Leiden Academic Centre for Drug Research, Leiden University, Leiden, 2333CC, the Netherlands.
| | - Alireza Mashaghi
- Medical Systems Biophysics and Bioengineering, Systems Pharmacology and Pharmacy Division, Leiden Academic Centre for Drug Research, Leiden University, Leiden, 2333CC, the Netherlands.
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