1
|
Soyer SM, Ozbek P, Kasavi C. Lung Adenocarcinoma Systems Biomarker and Drug Candidates Identified by Machine Learning, Gene Expression Data, and Integrative Bioinformatics Pipeline. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:408-420. [PMID: 38979602 DOI: 10.1089/omi.2024.0121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Lung adenocarcinoma (LUAD) is a significant planetary health challenge with its high morbidity and mortality rate, not to mention the marked interindividual variability in treatment outcomes and side effects. There is an urgent need for robust systems biomarkers that can help with early cancer diagnosis, prediction of treatment outcomes, and design of precision/personalized medicines for LUAD. The present study aimed at systems biomarkers of LUAD and deployed integrative bioinformatics and machine learning tools to harness gene expression data. Predictive models were developed to stratify patients based on prognostic outcomes. Importantly, we report here several potential key genes, for example, PMEL and BRIP1, and pathways implicated in the progression and prognosis of LUAD that could potentially be targeted for precision/personalized medicine in the future. Our drug repurposing analysis and molecular docking simulations suggested eight drug candidates for LUAD such as heat shock protein 90 inhibitors, cardiac glycosides, an antipsychotic agent (trifluoperazine), and a calcium ionophore (ionomycin). In summary, this study identifies several promising leads on systems biomarkers and drug candidates for LUAD. The findings also attest to the importance of integrative bioinformatics, structural biology and machine learning techniques in biomarker discovery, and precision oncology research and development.
Collapse
Affiliation(s)
- Semra Melis Soyer
- Department of Bioengineering, Faculty of Engineering, Marmara University, İstanbul, Türkiye
| | - Pemra Ozbek
- Department of Bioengineering, Faculty of Engineering, Marmara University, İstanbul, Türkiye
| | - Ceyda Kasavi
- Department of Bioengineering, Faculty of Engineering, Marmara University, İstanbul, Türkiye
| |
Collapse
|
2
|
Dessai A, Nayak UY, Nayak Y. Precision nanomedicine to treat non-small cell lung cancer. Life Sci 2024; 346:122614. [PMID: 38604287 DOI: 10.1016/j.lfs.2024.122614] [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: 02/14/2024] [Revised: 03/30/2024] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Lung cancer is a major cause of death worldwide, being often detected at a later stage due to the non-appearance of early symptoms. Therefore, specificity of the treatment is of utmost importance for its effective treatment. Precision medicine is a personalized therapy based on the genomics of the patient to design a suitable drug approach. Genetic mutations render the tumor resistant to specific mutations and the therapy is in vain even though correct medications are prescribed. Therefore, Precision medicine needs to be explored for the treatment of Non-small cell lung cancer (NSCLC). Nanoparticles are widely explored to give personalized interventions to treat lung cancer due to their various advantages like the ability to reach cancer cells, enhanced permeation through tissues, specificity, increased bioavailability, etc. Various nanoparticles (NPs) including gold nanoparticles, carbon nanotubes, aptamer-based NPs etc. were conjugated with biomarkers/diagnostic agents specific to cancer type and were delivered. Various biomarker genes have been identified through precision techniques for the diagnosis and treatment of NSCLC like EGFR, RET, KRAS, ALK, ROS-1, NTRK-1, etc. By incorporating of drug with the nanoparticle through bioconjugation, the specificity of the treatment can be enhanced with this revolutionary treatment. Additionally, integration of theranostic cargos in the nanoparticle would allow diagnosis as well as treatment by targeting the site of disease progression. Therefore, to target NSCLC effectively precision nanomedicine has been adopted in recent times. Here, we present different nanoparticles that are used as precision nanomedicine and their effectiveness against NSCLC disease.
Collapse
Affiliation(s)
- Akanksha Dessai
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Usha Yogendra Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
| | - Yogendra Nayak
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| |
Collapse
|
3
|
Gálffy G, Morócz É, Korompay R, Hécz R, Bujdosó R, Puskás R, Lovas T, Gáspár E, Yahya K, Király P, Lohinai Z. Targeted therapeutic options in early and metastatic NSCLC-overview. Pathol Oncol Res 2024; 30:1611715. [PMID: 38605928 PMCID: PMC11006988 DOI: 10.3389/pore.2024.1611715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/21/2024] [Indexed: 04/13/2024]
Abstract
The complex therapeutic strategy of non-small cell lung cancer (NSCLC) has changed significantly in recent years. Disease-free survival increased significantly with immunotherapy and chemotherapy registered in perioperative treatments, as well as adjuvant registered immunotherapy and targeted therapy (osimertinib) in case of EGFR mutation. In oncogenic-addictive metastatic NSCLC, primarily in adenocarcinoma, the range of targeted therapies is expanding, with which the expected overall survival increases significantly, measured in years. By 2021, the FDA and EMA have approved targeted agents to inhibit EGFR activating mutations, T790 M resistance mutation, BRAF V600E mutation, ALK, ROS1, NTRK and RET fusion. In 2022, the range of authorized target therapies was expanded. With therapies that inhibit KRASG12C, EGFR exon 20, HER2 and MET. Until now, there was no registered targeted therapy for the KRAS mutations, which affect 30% of adenocarcinomas. Thus, the greatest expectation surrounded the inhibition of the KRAS G12C mutation, which occurs in ∼15% of NSCLC, mainly in smokers and is characterized by a poor prognosis. Sotorasib and adagrasib are approved as second-line agents after at least one prior course of chemotherapy and/or immunotherapy. Adagrasib in first-line combination with pembrolizumab immunotherapy proved more beneficial, especially in patients with high expression of PD-L1. In EGFR exon 20 insertion mutation of lung adenocarcinoma, amivantanab was registered for progression after platinum-based chemotherapy. Lung adenocarcinoma carries an EGFR exon 20, HER2 insertion mutation in 2%, for which the first targeted therapy is trastuzumab deruxtecan, in patients already treated with platinum-based chemotherapy. Two orally administered selective c-MET inhibitors, capmatinib and tepotinib, were also approved after chemotherapy in adenocarcinoma carrying MET exon 14 skipping mutations of about 3%. Incorporating reflex testing with next-generation sequencing (NGS) expands personalized therapies by identifying guideline-recommended molecular alterations.
Collapse
|
4
|
Lee J, Honjo M, Aihara M. A MEK inhibitor arrests the cell cycle of human conjunctival fibroblasts and improves the outcome of glaucoma filtration surgery. Sci Rep 2024; 14:1871. [PMID: 38253821 PMCID: PMC10803501 DOI: 10.1038/s41598-024-52359-y] [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: 11/09/2023] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Better agents are needed to improve glaucoma filtration surgery outcomes compared to current ones. The purpose of this study is to determine whether mitogen-activated protein kinase kinase (MEK) inhibitors can effectively arrest the cell cycle of human conjunctival fibroblasts (HCFs) and inhibit the formation of fibrosis and scarring following glaucoma filtration surgery. A cell counting kit‑8 assay revealed that the MEK inhibitor PD0325901 exhibited concentration-dependent growth inhibition of HCFs. Quantitative PCR, immunocytochemistry, and western blotting demonstrated decreased expression of proliferating cell nuclear antigen (PCNA) and cyclin D1 and increased expression of p27 in HCFs treated with PD0325901. Flow cytometry indicated that PD0325901 arrested the cell cycle of HCFs in the G0/1 phase. The cell-migration assay showed that HCF migration rate was significantly suppressed by PD0325901 exposure. Rabbits were divided into PD0325901-treatment and control groups, and glaucoma filtration surgery was performed. Although intraocular pressure did not differ between PD0325901-treatment and control groups, bleb height was greater in the treatment group. Histopathological evaluation revealed that fibrotic changes were significantly attenuated in the PD0325901-treatment group compared to the control group. In conclusion, the MEK inhibitor impedes HCF proliferation via cell-cycle arrest and may be beneficial for glaucoma filtration surgery by reducing bleb scarring.
Collapse
Affiliation(s)
- Jinhee Lee
- Department of Ophthalmology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Megumi Honjo
- Department of Ophthalmology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Makoto Aihara
- Department of Ophthalmology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo, 113-8655, Japan
| |
Collapse
|
5
|
Scattolin D, Scagliori E, Scapinello A, Fantin A, Guarneri V, Pasello G. Small bowel edema and lymphocytic duodenitis as severe reversible gastrointestinal toxicity of selpercatinib in RET fusion-positive non-small cell lung cancer: a case report. Front Oncol 2023; 13:1201599. [PMID: 37492479 PMCID: PMC10363725 DOI: 10.3389/fonc.2023.1201599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/20/2023] [Indexed: 07/27/2023] Open
Abstract
Introduction Rearranged during transfection (RET) gene rearrangements occur in 1%-2% of non-small cell lung cancer (NSCLC). Because of the results of the study LIBRETTO-001, selpercatinib has been approved as the first-line treatment for patients with RET fusion-positive advanced NSCLC. Selpercatinib demonstrated to be well tolerated. Despite this, gastrointestinal adverse events (AEs) are frequently reported, and no clinical-radiological and endoscopic features and their impact in terms of treatment discontinuations, interruptions, and dose reductions have been described so far. Case report A 37-year-old never-smoker woman was treated in our institution with selpercatinib for a RET fusion-positive NSCLC. After 9 months of treatment, the patient referred abdominal pain of grade (G) 2, associated with nausea of G2, bilious vomiting of G3, and weight loss of G1. At computed tomography scan, the presence of important bowel wall thickening, free ascitic fluid, mesenteric congestion, and stranding was detected. The patient underwent an anterograde enteroscopy extended to jejunum with detection of lymphocytic duodenitis with sub-mucosal edema. Selpercatinib treatment was temporary interrupted with complete resolution of the symptoms and then re-administered with dose reduction, without relapsed of the gastrointestinal toxicity after 120 days. Conclusion To our knowledge, this is the first case report of a patient with NSCLC treated with selpercatinib outside a clinical study who developed severe gastrointestinal toxicity characterized by small bowel edema and lymphocytic duodenitis, leading to treatment interruption and dose reduction. The gastrointestinal AE has been described by a radiological, endoscopic, and histopathological point of view. Further investigations are needed to better identify pathological mechanisms of gastrointestinal toxicity for an appropriate AE management.
Collapse
Affiliation(s)
- Daniela Scattolin
- Medical Oncology 2, Veneto Institute of Oncology (IOV), IRCCS, Padova, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Elena Scagliori
- Radiology Unit, Veneto Institute of Oncology (IOV), IRCCS, Padova, Italy
| | - Antonio Scapinello
- Pathology Unit, Veneto Institute of Oncology (IOV), IRCCS, Padova, Italy
| | - Alberto Fantin
- Gastroenterology Unit, Veneto Institute of Oncology (IOV), IRCCS, Padova, Italy
| | - Valentina Guarneri
- Medical Oncology 2, Veneto Institute of Oncology (IOV), IRCCS, Padova, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| | - Giulia Pasello
- Medical Oncology 2, Veneto Institute of Oncology (IOV), IRCCS, Padova, Italy
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy
| |
Collapse
|
6
|
De Giglio A, Ricciuti B, Metro G. The expanding scenario of advanced non-small-cell lung cancer between emerging evidence and clinical tasks. Drugs Context 2023; 12:2022-11-4. [PMID: 37168875 PMCID: PMC10166260 DOI: 10.7573/dic.2022-11-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 11/13/2022] [Indexed: 05/13/2023] Open
Abstract
This Editorial by De Giglio, Ricciuti and Metro introduces the series Treatment of advanced non-small-cell lung cancer: one size does not fit all: https://www.drugsincontext.com/special_issues/treatment-of-advanced-non-small-cell-lung-cancer-one-size-does-not-fit-all/.
Collapse
Affiliation(s)
- Andrea De Giglio
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
- Medical Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Biagio Ricciuti
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Giulio Metro
- Medical Oncology, Santa Maria Della Misericordia Hospital, Azienda Ospedaliera di Perugia, Perugia, Italy
| |
Collapse
|