1
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Özay B, Tükel EY, Ayna Duran G, Kiraz Y. Identification of potential inhibitors for drug resistance in acute lymphoblastic leukemia through differentially expressed gene analysis and in silico screening. Anal Biochem 2024; 694:115619. [PMID: 39025197 DOI: 10.1016/j.ab.2024.115619] [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: 05/13/2024] [Revised: 07/11/2024] [Accepted: 07/13/2024] [Indexed: 07/20/2024]
Abstract
Acute lymphoblastic leukemia (ALL) is a disease of lymphocyte origin predominantly diagnosed in children. While its 5-year survival rate is high, resistance to chemotherapy drugs is still an obstacle. Our aim is to determine differentially expressed genes (DEGs) related to Asparaginase, Daunorubicin, Prednisolone, and Vincristine resistance and identify potential inhibitors via docking. Three datasets were accessed from the Gene Expression Omnibus database; GSE635, GSE19143, and GSE22529. The microarray data was analyzed using R4.2.0 and Bioconductor packages, and pathway and protein-protein interaction analysis were performed. We identified 1294 upregulated DEGs, with 12 genes consistently upregulated in all four resistant groups. KEGG analysis revealed an association with the PI3K-Akt pathway. Among DEGs, 33 hub genes including MDM2 and USP7 were pinpointed. Within common genes, CLDN9 and HS3ST3A1 were subjected to molecular docking against 3556 molecules. Following ADMET analysis, three drugs emerged as potential inhibitors: Flunarizine, Talniflumate, and Eltrombopag. Molecular dynamics analysis for HS3ST3A1 indicated all candidates had the potential to overcome drug resistance, Eltrombopag displaying particularly promising results. This study promotes a further understanding of drug resistance in ALL, introducing novel genes for consideration in diagnostic screening. It also presents potential inhibitor candidates to tackle drug resistance through repurposing.
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Affiliation(s)
- Başak Özay
- İzmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330, Balçova, Izmir, Turkey
| | - Ezgi Yağmur Tükel
- İzmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330, Balçova, Izmir, Turkey
| | - Gizem Ayna Duran
- İzmir University of Economics, Faculty of Engineering, Department of Biomedical Engineering, 35330, Balçova, Izmir, Turkey
| | - Yağmur Kiraz
- İzmir University of Economics, Faculty of Engineering, Department of Genetics and Bioengineering, 35330, Balçova, Izmir, Turkey.
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2
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Zyla J, Papiez A, Zhao J, Qu R, Li X, Kluger Y, Polanska J, Hatzis C, Pusztai L, Marczyk M. Evaluation of zero counts to better understand the discrepancies between bulk and single-cell RNA-Seq platforms. Comput Struct Biotechnol J 2023; 21:4663-4674. [PMID: 37841335 PMCID: PMC10568495 DOI: 10.1016/j.csbj.2023.09.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/17/2023] Open
Abstract
Recent advances in sample preparation and sequencing technology have made it possible to profile the transcriptomes of individual cells using single-cell RNA sequencing (scRNA-Seq). Compared to bulk RNA-Seq data, single-cell data often contain a higher percentage of zero reads, mainly due to lower sequencing depth per cell, which affects mostly measurements of low-expression genes. However, discrepancies between platforms are observed regardless of expression level. Using four paired datasets with multiple samples each, we investigated technical and biological factors that can contribute to this expression shift. Using two separate machine learning models we found that, in addition to expression level, RNA integrity, gene or UTR3 length, and the number of transcripts potentially also influence the occurrence of zeros. These findings could enable the development of novel analytical methods for cross-platform expression shift correction. We also identified genes and biological pathways in our diverse datasets that consistently showed differences when assessed at the single cell versus bulk level to assist in interpreting analysis across transcriptomic platforms. At the gene level, 25 genes (0.12%) were found in all datasets as discordant, but at the pathway level, 7 pathways (2.02%) showed shared enrichment in discordant genes.
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Affiliation(s)
- Joanna Zyla
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice 44-100, Poland
| | - Anna Papiez
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice 44-100, Poland
| | - Jun Zhao
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT 06510, USA
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Rihao Qu
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT 06510, USA
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Xiaotong Li
- Breast Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Yuval Kluger
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT 06510, USA
- Department of Pathology, Yale School of Medicine, Yale University, New Haven, CT 06510, USA
- Applied Mathematics Program, Yale University, New Haven, CT, USA
| | - Joanna Polanska
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice 44-100, Poland
| | - Christos Hatzis
- Breast Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Lajos Pusztai
- Breast Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Michal Marczyk
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice 44-100, Poland
- Breast Medical Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
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3
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Ochoa S, Hernández-Lemus E. Molecular mechanisms of multi-omic regulation in breast cancer. Front Oncol 2023; 13:1148861. [PMID: 37564937 PMCID: PMC10411627 DOI: 10.3389/fonc.2023.1148861] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023] Open
Abstract
Breast cancer is a complex disease that is influenced by the concurrent influence of multiple genetic and environmental factors. Recent advances in genomics and other high throughput biomolecular techniques (-omics) have provided numerous insights into the molecular mechanisms underlying breast cancer development and progression. A number of these mechanisms involve multiple layers of regulation. In this review, we summarize the current knowledge on the role of multiple omics in the regulation of breast cancer, including the effects of DNA methylation, non-coding RNA, and other epigenomic changes. We comment on how integrating such diverse mechanisms is envisioned as key to a more comprehensive understanding of breast carcinogenesis and cancer biology with relevance to prognostics, diagnostics and therapeutics. We also discuss the potential clinical implications of these findings and highlight areas for future research. Overall, our understanding of the molecular mechanisms of multi-omic regulation in breast cancer is rapidly increasing and has the potential to inform the development of novel therapeutic approaches for this disease.
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Affiliation(s)
- Soledad Ochoa
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Department of Obstetrics and Gynecology, Cedars-Sinai Medical Center, Los Angeles, CA, United States
| | - Enrique Hernández-Lemus
- Computational Genomics Division, National Institute of Genomic Medicine, Mexico City, Mexico
- Center for Complexity Sciences, Universidad Nacional Autónoma de México, Mexico City, Mexico
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4
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de Paula B, Kieran R, Koh SSY, Crocamo S, Abdelhay E, Muñoz-Espín D. Targeting Senescence as a Therapeutic Opportunity for Triple-Negative Breast Cancer. Mol Cancer Ther 2023; 22:583-598. [PMID: 36752780 PMCID: PMC10157365 DOI: 10.1158/1535-7163.mct-22-0643] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/21/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023]
Abstract
Triple-negative breast cancer (TNBC) is associated with an elevated risk of recurrence and poor prognosis. Historically, only chemotherapy was available as systemic treatment, but immunotherapy and targeted therapies currently offer prolonged benefits. TNBC is a group of diseases with heterogeneous treatment sensitivity, and resistance is inevitable and early for a large proportion of the intrinsic subtypes. Although senescence induction by anticancer therapy offers an immediate favorable clinical outcome once the rate of tumor progression reduces, these cells are commonly dysfunctional and metabolically active, culminating in treatment-resistant repopulation associated with worse prognosis. This heterogeneous response can also occur without therapeutic pressure in response to damage or oncogenic stress, playing a relevant role in the carcinogenesis. Remarkably, there is preclinical and exploratory clinical evidence to support a relevant role of senescence in treatment resistance. Therefore, targeting senescent cells has been a scientific effort in many malignant tumors using a variety of targets and strategies, including increasing proapoptotic and decreasing antiapoptotic stimuli. Despite promising results, there are some challenges to applying this technology, including the best schedule of combination, assessment of senescence, specific vulnerabilities, and the best clinical scenarios. This review provides an overview of senescence in TNBC with a focus on future-proofing senotherapy strategies.
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Affiliation(s)
- Bruno de Paula
- Breast Cancer Research Unit, Instituto Nacional de Cancer, Rio de Janeiro, Brazil
| | - Rosalind Kieran
- Early Cancer Institute, Department of Oncology, Cambridge University Hospitals Foundation Trust, Cambridge, United Kingdom
| | - Samantha Shui Yuan Koh
- Department of Medicine, Cambridge University Hospitals Foundation Trust, Cambridge, United Kingdom
| | - Susanne Crocamo
- Breast Cancer Research Unit, Instituto Nacional de Cancer, Rio de Janeiro, Brazil
| | | | - Daniel Muñoz-Espín
- Early Cancer Institute, Department of Oncology, Cambridge University Hospitals Foundation Trust, Cambridge, United Kingdom
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5
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Kujawa T, Marczyk M, Polanska J. Influence of single-cell RNA sequencing data integration on the performance of differential gene expression analysis. Front Genet 2022; 13:1009316. [PMID: 36386846 PMCID: PMC9663917 DOI: 10.3389/fgene.2022.1009316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/13/2022] [Indexed: 12/02/2022] Open
Abstract
Large-scale comprehensive single-cell experiments are often resource-intensive and require the involvement of many laboratories and/or taking measurements at various times. This inevitably leads to batch effects, and systematic variations in the data that might occur due to different technology platforms, reagent lots, or handling personnel. Such technical differences confound biological variations of interest and need to be corrected during the data integration process. Data integration is a challenging task due to the overlapping of biological and technical factors, which makes it difficult to distinguish their individual contribution to the overall observed effect. Moreover, the choice of integration method may impact the downstream analyses, including searching for differentially expressed genes. From the existing data integration methods, we selected only those that return the full expression matrix. We evaluated six methods in terms of their influence on the performance of differential gene expression analysis in two single-cell datasets with the same biological study design that differ only in the way the measurement was done: one dataset manifests strong batch effects due to the measurements of each sample at a different time. Integrated data were visualized using the UMAP method. The evaluation was done both on individual gene level using parametric and non-parametric approaches for finding differentially expressed genes and on gene set level using gene set enrichment analysis. As an evaluation metric, we used two correlation coefficients, Pearson and Spearman, of the obtained test statistics between reference, test, and corrected studies. Visual comparison of UMAP plots highlighted ComBat-seq, limma, and MNN, which reduced batch effects and preserved differences between biological conditions. Most of the tested methods changed the data distribution after integration, which negatively impacts the use of parametric methods for the analysis. Two algorithms, MNN and Scanorama, gave very poor results in terms of differential analysis on gene and gene set levels. Finally, we highlight ComBat-seq as it led to the highest correlation of test statistics between reference and corrected dataset among others. Moreover, it does not distort the original distribution of gene expression data, so it can be used in all types of downstream analyses.
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Affiliation(s)
- Tomasz Kujawa
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Michał Marczyk
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Joanna Polanska
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
- *Correspondence: Joanna Polanska,
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6
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Marczyk M, Macioszek A, Tobiasz J, Polanska J, Zyla J. Importance of SNP Dependency Correction and Association Integration for Gene Set Analysis in Genome-Wide Association Studies. Front Genet 2021; 12:767358. [PMID: 34956320 PMCID: PMC8696167 DOI: 10.3389/fgene.2021.767358] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
A typical genome-wide association study (GWAS) analyzes millions of single-nucleotide polymorphisms (SNPs), several of which are in a region of the same gene. To conduct gene set analysis (GSA), information from SNPs needs to be unified at the gene level. A widely used practice is to use only the most relevant SNP per gene; however, there are other methods of integration that could be applied here. Also, the problem of nonrandom association of alleles at two or more loci is often neglected. Here, we tested the impact of incorporation of different integrations and linkage disequilibrium (LD) correction on the performance of several GSA methods. Matched normal and breast cancer samples from The Cancer Genome Atlas database were used to evaluate the performance of six GSA algorithms: Coincident Extreme Ranks in Numerical Observations (CERNO), Gene Set Enrichment Analysis (GSEA), GSEA-SNP, improved GSEA for GWAS (i-GSEA4GWAS), Meta-Analysis Gene-set Enrichment of variaNT Associations (MAGENTA), and Over-Representation Analysis (ORA). Association of SNPs to phenotype was calculated using modified McNemar's test. Results for SNPs mapped to the same gene were integrated using Fisher and Stouffer methods and compared with the minimum p-value method. Four common measures were used to quantify the performance of all combinations of methods. Results of GSA analysis on GWAS were compared to the one performed on gene expression data. Comparing all evaluation metrics across different GSA algorithms, integrations, and LD correction, we highlighted CERNO, and MAGENTA with Stouffer as the most efficient. Applying LD correction increased prioritization and specificity of enrichment outcomes for all tested algorithms. When Fisher or Stouffer were used with LD, sensitivity and reproducibility were also better. Using any integration method was beneficial in comparison with a minimum p-value method in specific combinations. The correlation between GSA results from genomic and transcriptomic level was the highest when Stouffer integration was combined with LD correction. We thoroughly evaluated different approaches to GSA in GWAS in terms of performance to guide others to select the most effective combinations. We showed that LD correction and Stouffer integration could increase the performance of enrichment analysis and encourage the usage of these techniques.
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Affiliation(s)
- Michal Marczyk
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland.,Yale Cancer Center, Yale School of Medicine, New Haven, CT, United States
| | - Agnieszka Macioszek
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Joanna Tobiasz
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Joanna Polanska
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
| | - Joanna Zyla
- Department of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland
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7
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Jung HD, Sung YJ, Kim HU. Omics and Computational Modeling Approaches for the Effective Treatment of Drug-Resistant Cancer Cells. Front Genet 2021; 12:742902. [PMID: 34691155 PMCID: PMC8527086 DOI: 10.3389/fgene.2021.742902] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/20/2021] [Indexed: 02/05/2023] Open
Abstract
Chemotherapy is a mainstream cancer treatment, but has a constant challenge of drug resistance, which consequently leads to poor prognosis in cancer treatment. For better understanding and effective treatment of drug-resistant cancer cells, omics approaches have been widely conducted in various forms. A notable use of omics data beyond routine data mining is to use them for computational modeling that allows generating useful predictions, such as drug responses and prognostic biomarkers. In particular, an increasing volume of omics data has facilitated the development of machine learning models. In this mini review, we highlight recent studies on the use of multi-omics data for studying drug-resistant cancer cells. We put a particular focus on studies that use computational models to characterize drug-resistant cancer cells, and to predict biomarkers and/or drug responses. Computational models covered in this mini review include network-based models, machine learning models and genome-scale metabolic models. We also provide perspectives on future research opportunities for combating drug-resistant cancer cells.
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Affiliation(s)
- Hae Deok Jung
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Yoo Jin Sung
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.,KAIST Institute for Artificial Intelligence, KAIST, Daejeon, South Korea.,BioProcess Engineering Research Center and BioInformatics Research Center KAIST, Daejeon, South Korea
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8
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Anuraga G, Wang WJ, Phan NN, An Ton NT, Ta HDK, Berenice Prayugo F, Minh Xuan DT, Ku SC, Wu YF, Andriani V, Athoillah M, Lee KH, Wang CY. Potential Prognostic Biomarkers of NIMA (Never in Mitosis, Gene A)-Related Kinase (NEK) Family Members in Breast Cancer. J Pers Med 2021; 11:1089. [PMID: 34834441 PMCID: PMC8625415 DOI: 10.3390/jpm11111089] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 02/06/2023] Open
Abstract
Breast cancer remains the most common malignant cancer in women, with a staggering incidence of two million cases annually worldwide; therefore, it is crucial to explore novel biomarkers to assess the diagnosis and prognosis of breast cancer patients. NIMA-related kinase (NEK) protein kinase contains 11 family members named NEK1-NEK11, which were discovered from Aspergillus Nidulans; however, the role of NEK family genes for tumor development remains unclear and requires additional study. In the present study, we investigate the prognosis relationships of NEK family genes for breast cancer development, as well as the gene expression signature via the bioinformatics approach. The results of several integrative analyses revealed that most of the NEK family genes are overexpressed in breast cancer. Among these family genes, NEK2/6/8 overexpression had poor prognostic significance in distant metastasis-free survival (DMFS) in breast cancer patients. Meanwhile, NEK2/6 had the highest level of DNA methylation, and the functional enrichment analysis from MetaCore and Gene Set Enrichment Analysis (GSEA) suggested that NEK2 was associated with the cell cycle, G2M checkpoint, DNA repair, E2F, MYC, MTORC1, and interferon-related signaling. Moreover, Tumor Immune Estimation Resource (TIMER) results showed that the transcriptional levels of NEK2 were positively correlated with immune infiltration of B cells and CD4+ T Cell. Collectively, the current study indicated that NEK family genes, especially NEK2 which is involved in immune infiltration, and may serve as prognosis biomarkers for breast cancer progression.
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Affiliation(s)
- Gangga Anuraga
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia;
| | - Wei-Jan Wang
- Research Center for Cancer Biology, Department of Biological Science and Technology, China Medical University, Taichung 40604, Taiwan;
| | - Nam Nhut Phan
- Institute for Environmental Science, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; (N.N.P.); (N.T.A.T.)
| | - Nu Thuy An Ton
- Institute for Environmental Science, Nguyen Tat Thanh University, Ho Chi Minh City 700000, Vietnam; (N.N.P.); (N.T.A.T.)
| | - Hoang Dang Khoa Ta
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Fidelia Berenice Prayugo
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Su-Chi Ku
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
| | - Yung-Fu Wu
- Department of Medical Research, Tri-Service General Hospital, School of Medicine, National Defense Medical Center, Taipei 11490, Taiwan;
| | - Vivin Andriani
- Department of Biological Science, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia;
| | - Muhammad Athoillah
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia;
| | - Kuen-Haur Lee
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
| | - Chih-Yang Wang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (G.A.); (H.D.K.T.); (K.-H.L.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (F.B.P.); (D.T.M.X.); (S.-C.K.)
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Gangapuram M, Mazzio EA, Redda KK, Soliman KFA. Transcriptome Profile Analysis of Triple-Negative Breast Cancer Cells in Response to a Novel Cytostatic Tetrahydroisoquinoline Compared to Paclitaxel. Int J Mol Sci 2021; 22:ijms22147694. [PMID: 34299315 PMCID: PMC8306781 DOI: 10.3390/ijms22147694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/09/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022] Open
Abstract
The absence of chemotherapeutic target hormone receptors in breast cancer is descriptive of the commonly known triple-negative breast cancer (TNBC) subtype. TNBC remains one of the most aggressive invasive breast cancers, with the highest mortality rates in African American women. Therefore, new drug therapies are continually being explored. Microtubule-targeting agents such as paclitaxel (Taxol) interfere with microtubules dynamics, induce mitotic arrest, and remain a first-in-class adjunct drug to treat TNBC. Recently, we synthesized a series of small molecules of substituted tetrahydroisoquinolines (THIQs). The lead compound of this series, with the most potent cytostatic effect, was identified as 4-Ethyl-N-(7-hydroxy-3,4-dihydroisoquinolin-2(1H)-yl) benzamide (GM-4-53). In our previous work, GM-4-53 was similar to paclitaxel in its capacity to completely abrogate cell cycle in MDA-MB-231 TNBC cells, with the former not impairing tubulin depolymerization. Given that GM-4-53 is a cytostatic agent, and little is known about its mechanism of action, here, we elucidate differences and similarities to paclitaxel by evaluating whole-transcriptome microarray data in MDA-MB-231 cells. The data obtained show that both drugs were cytostatic at non-toxic concentrations and caused deformed morphological cytoskeletal enlargement in 2D cultures. In 3D cultures, the data show greater core penetration, observed by GM-4-53, than paclitaxel. In concentrations where the drugs entirely blocked the cell cycle, the transcriptome profile of the 48,226 genes analyzed (selection criteria: (p-value, FDR p-value < 0.05, fold change −2< and >2)), paclitaxel evoked 153 differentially expressed genes (DEGs), GM-4-53 evoked 243 DEGs, and, of these changes, 52/153 paclitaxel DEGs were also observed by GM-4-53, constituting a 34% overlap. The 52 DEGS analysis by String database indicates that these changes involve transcripts that influence microtubule spindle formation, chromosome segregation, mitosis/cell cycle, and transforming growth factor-β (TGF-β) signaling. Of interest, both drugs effectively downregulated “inhibitor of DNA binding, dominant negative helix-loop-helix” (ID) transcripts; ID1, ID3 and ID4, and amphiregulin (AREG) and epiregulin (EREG) transcripts, which play a formidable role in cell division. Given the efficient solubility of GM-4-53, its low molecular weight (MW; 296), and capacity to penetrate a small solid tumor mass and effectively block the cell cycle, this drug may have future therapeutic value in treating TNBC or other cancers. Future studies will be required to evaluate this drug in preclinical models.
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10
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Li Y, Li Z. Potential Mechanism Underlying the Role of Mitochondria in Breast Cancer Drug Resistance and Its Related Treatment Prospects. Front Oncol 2021; 11:629614. [PMID: 33816265 PMCID: PMC8013997 DOI: 10.3389/fonc.2021.629614] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/03/2021] [Indexed: 12/22/2022] Open
Abstract
Breast cancer incidence and mortality rates have been consistently high among women. The use of diverse therapeutic strategies, including chemotherapy, endocrine therapy, targeted therapy, and immunotherapy, has improved breast cancer prognosis. However, drug resistance has become a tremendous obstacle in overcoming breast cancer recurrence and metastasis. It is known that mitochondria play an important role in carcinoma cell growth, invasion and apoptosis. Recent studies have explored the involvement of mitochondrial metabolism in breast cancer prognosis. Here, we will provide an overview of studies that investigated mitochondrial metabolism pathways in breast cancer treatment resistance, and discuss the application prospects of agents targeting mitochondrial pathways against drug-resistant breast cancer.
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Affiliation(s)
- Yuefeng Li
- Department of Oncological Surgery, Shaoxing Second Hospital, Shaoxing, China
| | - Zhian Li
- Department of Oncological Surgery, Shaoxing Second Hospital, Shaoxing, China
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11
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Sitia L, Bonizzi A, Mazzucchelli S, Negri S, Sottani C, Grignani E, Rizzuto MA, Prosperi D, Sorrentino L, Morasso C, Allevi R, Sevieri M, Silva F, Truffi M, Corsi F. Selective Targeting of Cancer-Associated Fibroblasts by Engineered H-Ferritin Nanocages Loaded with Navitoclax. Cells 2021; 10:328. [PMID: 33562504 PMCID: PMC7915356 DOI: 10.3390/cells10020328] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/29/2021] [Accepted: 02/02/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer-associated fibroblasts (CAFs) are key actors in regulating cancer progression. They promote tumor growth, metastasis formation, and induce drug resistance. For these reasons, they are emerging as potential therapeutic targets. Here, with the aim of developing CAF-targeted drug delivery agents, we functionalized H-ferritin (HFn) nanocages with fibroblast activation protein (FAP) antibody fragments. Functionalized nanocages (HFn-FAP) have significantly higher binding with FAP+ CAFs than with FAP- cancer cells. We loaded HFn-FAP with navitoclax (Nav), an experimental Bcl-2 inhibitor pro-apoptotic drug, whose clinical development is limited by its strong hydrophobicity and toxicity. We showed that Nav is efficiently loaded into HFn (HNav), maintaining its mechanism of action. Incubating Nav-loaded functionalized nanocages (HNav-FAP) with FAP+ cells, we found significantly higher cytotoxicity as compared to non-functionalized HNav. This was correlated with a significantly higher drug release only in FAP+ cells, confirming the specific targeting ability of functionalized HFn. Finally, we showed that HFn-FAP is able to reach the tumor and to target CAFs in a mouse syngeneic model of triple negative breast cancer after intravenous administration. Our data show that HNav-FAP could be a promising tool to enhance specific drug delivery into CAFs, thus opening new therapeutic possibilities focused on tumor microenvironment.
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Affiliation(s)
- Leopoldo Sitia
- Dipartimento di Scienze Biomediche e Cliniche “L. Sacco”, Università di Milano, 20157 Milan, Italy; (L.S.); (A.B.); (S.M.); (R.A.); (M.S.); (F.S.)
| | - Arianna Bonizzi
- Dipartimento di Scienze Biomediche e Cliniche “L. Sacco”, Università di Milano, 20157 Milan, Italy; (L.S.); (A.B.); (S.M.); (R.A.); (M.S.); (F.S.)
| | - Serena Mazzucchelli
- Dipartimento di Scienze Biomediche e Cliniche “L. Sacco”, Università di Milano, 20157 Milan, Italy; (L.S.); (A.B.); (S.M.); (R.A.); (M.S.); (F.S.)
| | - Sara Negri
- Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy; (S.N.); (C.S.); (E.G.); (C.M.)
| | - Cristina Sottani
- Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy; (S.N.); (C.S.); (E.G.); (C.M.)
| | - Elena Grignani
- Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy; (S.N.); (C.S.); (E.G.); (C.M.)
| | - Maria Antonietta Rizzuto
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126 Milan, Italy; (M.A.R.); (D.P.)
| | - Davide Prosperi
- Department of Biotechnology and Biosciences, University of Milan-Bicocca, 20126 Milan, Italy; (M.A.R.); (D.P.)
| | - Luca Sorrentino
- Colorectal Surgery Unit, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, 20133 Milan, Italy;
| | - Carlo Morasso
- Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy; (S.N.); (C.S.); (E.G.); (C.M.)
| | - Raffaele Allevi
- Dipartimento di Scienze Biomediche e Cliniche “L. Sacco”, Università di Milano, 20157 Milan, Italy; (L.S.); (A.B.); (S.M.); (R.A.); (M.S.); (F.S.)
| | - Marta Sevieri
- Dipartimento di Scienze Biomediche e Cliniche “L. Sacco”, Università di Milano, 20157 Milan, Italy; (L.S.); (A.B.); (S.M.); (R.A.); (M.S.); (F.S.)
| | - Filippo Silva
- Dipartimento di Scienze Biomediche e Cliniche “L. Sacco”, Università di Milano, 20157 Milan, Italy; (L.S.); (A.B.); (S.M.); (R.A.); (M.S.); (F.S.)
| | - Marta Truffi
- Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy; (S.N.); (C.S.); (E.G.); (C.M.)
| | - Fabio Corsi
- Dipartimento di Scienze Biomediche e Cliniche “L. Sacco”, Università di Milano, 20157 Milan, Italy; (L.S.); (A.B.); (S.M.); (R.A.); (M.S.); (F.S.)
- Istituti Clinici Scientifici Maugeri IRCCS, 27100 Pavia, Italy; (S.N.); (C.S.); (E.G.); (C.M.)
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