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Causin RL, Polezi MR, Freitas AJAD, Calfa S, Altei WF, Dias JO, Laus AC, Pessôa-Pereira D, Komoto TT, Evangelista AF, Souza CDP, Reis RM, Marques MMC. EV-miRNAs from breast cancer patients of plasma as potential prognostic biomarkers of disease recurrence. Heliyon 2024; 10:e33933. [PMID: 39104474 PMCID: PMC11298852 DOI: 10.1016/j.heliyon.2024.e33933] [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: 10/20/2023] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 08/07/2024] Open
Abstract
Background Extracellular vesicles (EVs), ubiquitously released by blood cells, facilitate intercellular communication. In cancer, tumor-derived EVs profoundly affect the microenvironment, promoting tumor progression and raising the risk of recurrence. These EVs contain miRNAs (EV-miRNAs), promising cancer biomarkers. Characterizing plasma EVs and identifying EV-miRNAs associated with breast cancer recurrence are crucial aspects of cancer research since they allow us to discover new biomarkers that are effective for understanding tumor biology and for being used for early detection, disease monitoring, or approaches to personalized medicine. This study aimed to characterize plasma EVs in breast cancer (BC) patients and identify EV-miRNAs associated with BC recurrence. Methods This retrospective observational study included 24 BC patients divided into recurrence (n= 11) and non-recurrence (n= 13) groups. Plasma EVs were isolated and characterized. Total RNA from EVs was analyzed for miRNA expression using NanoString's nCounter® miRNA Expression Assays panel. MicroRNA target prediction used mirDIP, and pathway interactions were assessed via Reactome. Results A stronger presence of circulating EVs was found to be linked with a less favorable prognosis (p = 0.0062). We discovered a distinct signature of EV-miRNAs, notably including miR-19a-3p and miR-130b-3p, which are significantly associated with breast cancer recurrence. Furthermore, miR-19a-3p and miR-130b-3p were implicated in the regulation of PTEN and MDM4, potentially contributing to breast cancer progression.A notable association emerged, indicating a high concentration of circulating EVs predicts poor prognosis (p = 0.0062). Our study found a distinct EV-miRNA signature involving miR-19a-3p and miR-130b-3p, strongly associated with disease recurrence. We also presented compelling evidence for their regulatory roles in PTEN and MDM4 genes, contributing to BC development. Conclusion This study revealed that increased plasma EV concentration is associated with BC recurrence. The prognostic significance of EVs is closely tied to the unique expression profiles of miR-19a-3p and miR-130b-3p. These findings underscore the potential of EV-associated miRNAs as valuable indicators for BC recurrence, opening new avenues for diagnosis and treatment exploration.
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Affiliation(s)
- Rhafaela Lima Causin
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Mariana Regatieri Polezi
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | | | - Stéphanie Calfa
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Wanessa Fernanda Altei
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
- Radiation Oncology Department, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Júlia Oliveira Dias
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Danielle Pessôa-Pereira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Tatiana Takahasi Komoto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
| | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
- Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Manguinhos, Rio de Janeiro, 21040-361, Brazil
| | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, 14784-400, Brazil
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, 4710-057, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga, 4710-057, Portugal
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Wehbe N, Badran A, Baydoun S, Al-Sawalmih A, Maresca M, Baydoun E, Mesmar JE. The Antioxidant Potential and Anticancer Activity of Halodule uninervis Ethanolic Extract against Triple-Negative Breast Cancer Cells. Antioxidants (Basel) 2024; 13:726. [PMID: 38929164 PMCID: PMC11200955 DOI: 10.3390/antiox13060726] [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: 04/28/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/28/2024] Open
Abstract
Natural remedies have been indispensable to traditional medicine practices for generations, offering therapeutic solutions for various ailments. In modern times, these natural products continue to play a pivotal role in the discovery of new drugs, especially for cancer treatment. The marine ecosystem offers a wide range of plants with potential anticancer activities due to their distinct biochemical diversity and adaptation to extreme situations. The seagrass Halodule uninervis is rich in diverse bioactive metabolites that bestow the plant with various pharmacological properties. However, its anticancer activity against invasive triple-negative breast cancer (TNBC) is still poorly investigated. In the present study, the phytochemical composition of an ethanolic extract of H. uninervis (HUE) was screened, and its antioxidant potential was evaluated. Moreover, the anticancer potential of HUE against MDA-MB-231 cells was investigated along with the possible underlying mechanisms of action. Our results showed that HUE is rich in diverse phytochemicals that are known for their antioxidant and anticancer effects. In MDA-MB-231 cells, HUE targeted the hallmarks of cancer, including cell proliferation, adhesion, migration, invasion, and angiogenesis. The HUE-mediated anti-proliferative and anti-metastatic effects were associated with the downregulation of the proto-oncogenic STAT3 signaling pathway. Taken together, H. uninervis could serve as a valuable source for developing novel drugs targeting TNBC.
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Affiliation(s)
- Nadine Wehbe
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Riad El Solh, Beirut 1107 2020, Lebanon; (N.W.); (E.B.)
| | - Adnan Badran
- Department of Nutrition, Faculty of Pharmacy and Medical Sciences, University of Petra, Amman 11196, Jordan;
| | - Serine Baydoun
- Breast Imaging Section, Imaging Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA;
| | - Ali Al-Sawalmih
- Marine Science Station, University of Jordan, Aqaba 11942, Jordan;
| | - Marc Maresca
- Aix-Marseille Univ, CNRS, Centrale Marseille, iSM2, 13013 Marseille, France
| | - Elias Baydoun
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Riad El Solh, Beirut 1107 2020, Lebanon; (N.W.); (E.B.)
| | - Joelle Edward Mesmar
- Department of Biology, Faculty of Arts and Sciences, American University of Beirut, Riad El Solh, Beirut 1107 2020, Lebanon; (N.W.); (E.B.)
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3
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Liang S, Xu S, Zhou S, Chang C, Shao Z, Wang Y, Chen S, Huang Y, Guo Y. IMAGGS: a radiogenomic framework for identifying multi-way associations in breast cancer subtypes. J Genet Genomics 2024; 51:443-453. [PMID: 37783335 DOI: 10.1016/j.jgg.2023.09.010] [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: 09/04/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023]
Abstract
Investigating correlations between radiomic and genomic profiling in breast cancer (BC) molecular subtypes is crucial for understanding disease mechanisms and providing personalized treatment. We present a well-designed radiogenomic framework image-gene-gene set (IMAGGS), which detects multi-way associations in BC subtypes by integrating radiomic and genomic features. Our dataset consists of 721 patients, each of whom has 12 ultrasound (US) images captured from different angles and gene mutation data. To better characterize tumor traits, 12 multi-angle US images are fused using two distinct strategies. Then, we analyze complex many-to-many associations between phenotypic and genotypic features using a machine learning algorithm, deviating from the prevalent one-to-one relationship pattern observed in previous studies. Key radiomic and genomic features are screened using these associations. In addition, gene set enrichment analysis is performed to investigate the joint effects of gene sets and delve deeper into the biological functions of BC subtypes. We further validate the feasibility of IMAGGS in a glioblastoma multiforme dataset to demonstrate the scalability of IMAGGS across different modalities and diseases. Taken together, IMAGGS provides a comprehensive characterization for diseases by associating imaging, genes, and gene sets, paving the way for biological interpretation of radiomics and development of targeted therapy.
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Affiliation(s)
- Shuyu Liang
- Department of Electronic Engineering, School of Information Science and Technology, Fudan University, Shanghai 200433, China; The Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention (MICCAI) of Shanghai, Shanghai 200032, China
| | - Sicheng Xu
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200433, China
| | - Shichong Zhou
- Department of Ultrasound, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Cai Chang
- Department of Ultrasound, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhiming Shao
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuanyuan Wang
- Department of Electronic Engineering, School of Information Science and Technology, Fudan University, Shanghai 200433, China; The Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention (MICCAI) of Shanghai, Shanghai 200032, China
| | - Sheng Chen
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Yunxia Huang
- Department of Ultrasound, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Yi Guo
- Department of Electronic Engineering, School of Information Science and Technology, Fudan University, Shanghai 200433, China; The Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention (MICCAI) of Shanghai, Shanghai 200032, China.
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4
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Taheri G, Habibi M. Uncovering driver genes in breast cancer through an innovative machine learning mutational analysis method. Comput Biol Med 2024; 171:108234. [PMID: 38430742 DOI: 10.1016/j.compbiomed.2024.108234] [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: 08/15/2023] [Revised: 01/25/2024] [Accepted: 02/25/2024] [Indexed: 03/05/2024]
Abstract
Breast cancer has become a severe public health concern and one of the leading causes of cancer-related death in women worldwide. Several genes and mutations in these genes linked to breast cancer have been identified using sophisticated techniques, despite the fact that the exact cause of breast cancer is still unknown. A commonly used feature for identifying driver mutations is the recurrence of a mutation in patients. Nevertheless, some mutations are more likely to occur than others for various reasons. Sequencing analysis has shown that cancer-driving genes operate across complex networks, often with mutations appearing in a modular pattern. In this work, as a retrospective study, we used TCGA data, which is gathered from breast cancer patients. We introduced a new machine-learning approach to examine gene functionality in networks derived from mutation associations, gene-gene interactions, and graph clustering for breast cancer analysis. These networks have uncovered crucial biological components in critical pathways, particularly those that exhibit low-frequency mutations. The statistical strength of the clinical study is significantly boosted by evaluating the network as a whole instead of just single gene effects. Our method successfully identified essential driver genes with diverse mutation frequencies. We then explored the functions of these potential driver genes and their related pathways. By uncovering low-frequency genes, we shed light on understudied pathways associated with breast cancer. Additionally, we present a novel Monte Carlo-based algorithm to identify driver modules in breast cancer. Our findings highlight the significance and role of these modules in critical signaling pathways in breast cancer, providing a comprehensive understanding of breast cancer development. Materials and implementations are available at: [https://github.com/MahnazHabibi/BreastCancer].
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Affiliation(s)
- Golnaz Taheri
- Department of Computer and Systems Sciences, Stockholm University, Stockholm, Sweden; Science for Life Laboratory, Stockholm, Sweden.
| | - Mahnaz Habibi
- Department of Mathematics, Qazvin Branch, Islamic Azad University, Qazvin, Iran
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5
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Schittenhelm MM, Kaiser M, Győrffy B, Kampa-Schittenhelm KM. Evaluation of apoptosis stimulating protein of TP53-1 (ASPP1/PPP1R13B) to predict therapy resistance and overall survival in acute myeloid leukemia (AML). Cell Death Dis 2024; 15:25. [PMID: 38195541 PMCID: PMC10776670 DOI: 10.1038/s41419-023-06372-0] [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: 07/06/2023] [Revised: 11/26/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024]
Abstract
ASPP1 (PPP1R13B) belongs to a family of p53-binding proteins and enhances apoptosis by stimulation of p53-transactivation of selected proapoptotic target genes. It is preferentially expressed in hematopoietic stem cells (HSC) and together with p53 preserves the genomic integrity of the HSC pool. Consequently, dysfunction of ASPP1 has been associated with malignant transformation and development of acute lymphoblastic leukemias and lymphomas - whereas methylation of the promoter region is linked to reduced transcription and ultimately attenuated expression of ASPP1. The role of ASPP1 in AML is not known. We now show that impaired regulation of PPP1R13B contributes to the biology of leukemogenesis and primary therapy resistance in AML. PPP1R13B mRNA expression patterns thereby define a distinct prognostic profile - which is not reflected by the European leukemia net (ELN) risk score. These findings have direct therapeutic implications and we provide a strategy to restore ASPP1 protein levels using hypomethylating agents to sensitize cells towards proapoptotic drugs. Prospective clinical trials are warranted to investigate the role of ASPP1 (PPP1R13B) as a biomarker for risk stratification and as a potential therapeutic target to restore susceptibility to chemotherapy.
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Affiliation(s)
- Marcus M Schittenhelm
- Medical research center (MFZ) and Clinic of Medical Oncology and Hematology, Cantonal Hospital St. Gallen (KSSG), St. Gallen, Switzerland
| | - Max Kaiser
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen (UKT), Tübingen, Germany
| | - Balázs Győrffy
- Semmelweis University Dept. of Bioinformatics and Dept. of Pediatrics, Budapest, H-1094, Hungary
- TTK Cancer Biomarker Research Group, Institute of Enzymology, Budapest, H-1117, Hungary
| | - Kerstin M Kampa-Schittenhelm
- Medical research center (MFZ) and Clinic of Medical Oncology and Hematology, Cantonal Hospital St. Gallen (KSSG), St. Gallen, Switzerland.
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tübingen (UKT), Tübingen, Germany.
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Mansour A, Fytory M, Ahmed OM, Rahman FEZSA, El-Sherbiny IM. In-vitro and in-vivo assessment of pH-responsive core-shell nanocarrier system for sequential delivery of methotrexate and 5-fluorouracil for the treatment of breast cancer. Int J Pharm 2023; 648:123608. [PMID: 37972670 DOI: 10.1016/j.ijpharm.2023.123608] [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: 07/30/2023] [Revised: 10/31/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Breast cancer (BC) is one of the leading fatal diseases affecting females worldwide. Despite the presence of tremendous chemotherapeutic agents, the resistance emergence directs the recent research towards synergistic drugs' combination along with encapsulation inside biocompatible smart nanocarriers. Methotrexate (MTX) and 5-fluorouracil (Fu) are effective against BC and have sequential synergistic activity. In this study, a core-shell nanocarrier composed of mesoporous silica nanoparticles (MSN) as the core and zeolitic imidazolate framework-8 nano metal organic frameworks (ZIF-8 NMOF) as the shell was developed and loaded with Fu and MTX, respectively. The developed nanostructure; Fu-MSN@MTX-NMOF was validated by several characterization techniques and conferred high drugs' entrapment efficiency (EE%). In-vitro assessment revealed a pH-responsive drug release pattern in the acidic pH where MTX was released followed by Fu. The cytotoxicity evaluation indicated enhanced anticancer effect of the Fu-MSN@MTX-NMOF relative to the free drugs in addition to time-dependent fortified cytotoxic effect due to the sequential drugs' release. The in-vivo anticancer efficiency was examined using Ehrlich ascites carcinoma (EAC) animal model where the anticancer effect of the developed Fu-MSN@MTX-NMOF was compared to the sequentially administrated free drugs. The results revealed enhanced anti-tumor effect while maintaining the normal functions of the vital organs as the heart, kidney and liver.
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Affiliation(s)
- Amira Mansour
- Nanomedicine Research Labs, Center for Materials Science (CMS), Zewail City of Science and Technology, 6(th) October City, 12578, Giza, Egypt
| | - Mostafa Fytory
- Nanomedicine Research Labs, Center for Materials Science (CMS), Zewail City of Science and Technology, 6(th) October City, 12578, Giza, Egypt; Material Science and Nanotechnology Department, Faculty of Postgraduate Studies for Advanced Sciences (PSAS), Beni-Suef University, 62511, Beni-suef, Egypt
| | - Osama M Ahmed
- Physiology Division, Zoology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62521, Egypt
| | | | - Ibrahim M El-Sherbiny
- Nanomedicine Research Labs, Center for Materials Science (CMS), Zewail City of Science and Technology, 6(th) October City, 12578, Giza, Egypt.
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7
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Zhou F, He K, Ni Y. Individualized causal discovery with latent trajectory embedded Bayesian networks. Biometrics 2023; 79:3191-3202. [PMID: 36807295 DOI: 10.1111/biom.13843] [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: 12/13/2021] [Revised: 12/08/2022] [Accepted: 02/06/2023] [Indexed: 02/20/2023]
Abstract
Bayesian networks have been widely used to generate causal hypotheses from multivariate data. Despite their popularity, the vast majority of existing causal discovery approaches make the strong assumption of a (partially) homogeneous sampling scheme. However, such assumption can be seriously violated, causing significant biases when the underlying population is inherently heterogeneous. To this end, we propose a novel causal Bayesian network model, termed BN-LTE, that embeds heterogeneous samples onto a low-dimensional manifold and builds Bayesian networks conditional on the embedding. This new framework allows for more precise network inference by improving the estimation resolution from the population level to the observation level. Moreover, while causal Bayesian networks are in general not identifiable with purely observational, cross-sectional data due to Markov equivalence, with the blessing of causal effect heterogeneity, we prove that the proposed BN-LTE is uniquely identifiable under relatively mild assumptions. Through extensive experiments, we demonstrate the superior performance of BN-LTE in causal structure learning as well as inferring observation-specific gene regulatory networks from observational data.
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Affiliation(s)
- Fangting Zhou
- Institute of Statistics and Big Data, Renmin University of China, Beijing, China
- Department of Statistics, Texas A&M University, College Station, Texas, USA
| | - Kejun He
- Institute of Statistics and Big Data, Renmin University of China, Beijing, China
| | - Yang Ni
- Department of Statistics, Texas A&M University, College Station, Texas, USA
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Guo H, Lv X, Li Y, Li M. Attention-based GCN integrates multi-omics data for breast cancer subtype classification and patient-specific gene marker identification. Brief Funct Genomics 2023; 22:463-474. [PMID: 37114942 DOI: 10.1093/bfgp/elad013] [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: 02/16/2023] [Accepted: 03/17/2023] [Indexed: 04/29/2023] Open
Abstract
Breast cancer is a heterogeneous disease and can be divided into several subtypes with unique prognostic and molecular characteristics. The classification of breast cancer subtypes plays an important role in the precision treatment and prognosis of breast cancer. Benefitting from the relation-aware ability of a graph convolution network (GCN), we present a multi-omics integrative method, the attention-based GCN (AGCN), for breast cancer molecular subtype classification using messenger RNA expression, copy number variation and deoxyribonucleic acid methylation multi-omics data. In the extensive comparative studies, our AGCN models outperform state-of-the-art methods under different experimental conditions and both attention mechanisms and the graph convolution subnetwork play an important role in accurate cancer subtype classification. The layer-wise relevance propagation (LRP) algorithm is used for the interpretation of model decision, which can identify patient-specific important biomarkers that are reported to be related to the occurrence and development of breast cancer. Our results highlighted the effectiveness of the GCN and attention mechanisms in multi-omics integrative analysis and the implement of the LRP algorithm can provide biologically reasonable insights into model decision.
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Affiliation(s)
- Hui Guo
- College of Chemistry at Sichuan University
| | - Xiang Lv
- College of Chemistry at Sichuan University
| | - Yizhou Li
- College of Cyber Science and Engineering at Sichuan University
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Milliana A, Listiyana A, Mutiah R, Annisa R, Firdausi AF, Faradila VA, Febriani A, Ainina EI, Nabila Kirana NL, Yueniwati Y. The Potential of Eleutherine bulbosa in Inducing Apoptosis and Inhibiting Cell Cycle in Breast Cancer: A Network Pharmacology Approach and In Vitro Experiments. Asian Pac J Cancer Prev 2023; 24:3783-3794. [PMID: 38019236 PMCID: PMC10772747 DOI: 10.31557/apjcp.2023.24.11.3783] [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: 05/26/2023] [Accepted: 11/10/2023] [Indexed: 11/30/2023] Open
Abstract
OBJECTIVE The objective of this study was to evaluate the potential and mechanisms of phytochemicals in Eleutherine bulbosa (EBE) in inducing apoptosis and inhibiting the cell cycle in breast cancer through a network pharmacology approach and in vitro validation. METHODS This research employed a literature review approach to identify active anti-cancer compounds and utilized a network pharmacology approach to predict the mechanisms of action of EBE compounds in breast cancer. In addition, in vitro experiments were conducted using MTT method to evaluate the effects of EBE on the cytotoxicity of T47D cells, and the flow cytometry method was employed to determine the impact of EBE on apoptosis and the cell cycle. RESULTS The network pharmacology analysis revealed that EBE had an impact on 42 genes involved in breast cancer, including 23 important target genes implicated in the pathophysiology of breast cancer. Pathway analysis using the KEGG database showed a close association between EBE and crucial signaling pathways in breast cancer, including P53 signaling pathway, MAPK signaling pathway, PI3K-Akt signaling pathway, apoptosis and cell cycle. In vitro experiments demonstrated that EBE exhibited moderate anti-cancer activity. Furthermore, EBE demonstrated significant potential in inducing apoptosis in breast cancer cells, with a percentage of apoptotic cells reaching 93.6%. Additionally, EBE was observed to disrupt the cell cycle, leading to a significant increase in the sub G1 and S phases, and a significant decrease in the G2-M and G1 phases. CONCLUSION EBE has the potential to be an anti-cancer agent through various mechanisms, including apoptosis induction and cell cycle inhibition in breast cancer cells. These findings provide new insights into the potential of EBE as an alternative treatment for breast cancer.
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Affiliation(s)
- Alvi Milliana
- Department of Medicine, Faculty of Medicine and Health Sciences, UIN Maulana Malik Ibrahim Malang, East Java, Indonesia.
| | - Anik Listiyana
- Department of Medicine, Faculty of Medicine and Health Sciences, UIN Maulana Malik Ibrahim Malang, East Java, Indonesia.
| | - Roihatul Mutiah
- Department of Pharmacy, Faculty of Medicine and Health Sciences, UIN Maulana Malik Ibrahim Malang, East Java, Indonesia.
| | - Rahmi Annisa
- Department of Pharmacy, Faculty of Medicine and Health Sciences, UIN Maulana Malik Ibrahim Malang, East Java, Indonesia.
| | - Alif Firman Firdausi
- Department of Pharmacy, Faculty of Medicine and Health Sciences, UIN Maulana Malik Ibrahim Malang, East Java, Indonesia.
| | - Vira Azzara Faradila
- Department of Pharmacy, Faculty of Medicine and Health Sciences, UIN Maulana Malik Ibrahim Malang, East Java, Indonesia.
| | - Anisa Febriani
- Department of Pharmacy, Faculty of Medicine and Health Sciences, UIN Maulana Malik Ibrahim Malang, East Java, Indonesia.
| | - Elsa Iftita Ainina
- Department of Pharmacy, Faculty of Medicine and Health Sciences, UIN Maulana Malik Ibrahim Malang, East Java, Indonesia.
| | - Nariswari Lutfi Nabila Kirana
- Department of Pharmacy, Faculty of Medicine and Health Sciences, UIN Maulana Malik Ibrahim Malang, East Java, Indonesia.
| | - Yuyun Yueniwati
- Department of Medicine, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia, East Java, Indonesia.
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Kumar U, Aich J, Devarajan S. Exploring the repurposing potential of telmisartan drug in breast cancer: an in-silico and in-vitro approach. Anticancer Drugs 2023; 34:1094-1103. [PMID: 36847075 DOI: 10.1097/cad.0000000000001509] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Anticancer drug resistance is one of the biggest hurdles in the treatment of breast cancer. Drug repurposing is a viable option fordeveloping novel medical treatment strategies since this method is more cost-efficient and rapid. Antihypertensive medicines have recently been found to have pharmacological features that could be used to treat cancer, making them effective candidates for therapeutic repurposing. The goal of our research is to find a potent antihypertensive drug that can be repurposed as adjuvant therapy for breast cancer. In this study, virtual screening was performed using a set of Food and Drug Administration (FDA)-approved antihypertensive drugs as ligands with selected receptor proteins (EGFR, KRAS, P53, AGTR1, AGTR2, and ACE) assuming these proteins are regarded to have a significant role in hypertension as well as breast cancer. Further, our in-silico results were further confirmed by an in-vitro experiment (cytotoxicity assay). All the compounds (enalapril, atenolol, acebutolol, propranolol, amlodipine, verapamil, doxazosin, prazosin, hydralazine, irbesartan, telmisartan, candesartan, and aliskiren) showed remarkable affinity towards the target receptor proteins. However, maximum affinity was displayed by telmisartan. Cell-based cytotoxicity study of telmisartan in MCF7 (breast cancer cell line) confirmed the anticancer effect of telmisartan. IC50 of the drug was calculated to be 7.75 µM and at this concentration, remarkable morphological alterations were observed in the MCF7 cells confirming its cytotoxicity in breast cancer cells. Based on both in-silico and in-vitro studies, we can conclude that telmisartan appears to be a promising drug repurposing candidate for the therapeutic treatment of breast cancer.
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Affiliation(s)
- Urwashi Kumar
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to Be University, CBD Belapur, Navi Mumbai, Maharashtra, India
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Alves-Vale C, Capela AM, Tavares-Marcos C, Domingues-Silva B, Pereira B, Santos F, Gomes CP, Espadas G, Vitorino R, Sabidó E, Borralho P, Nóbrega-Pereira S, Bernardes de Jesus B. Expression of NORAD correlates with breast cancer aggressiveness and protects breast cancer cells from chemotherapy. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:910-924. [PMID: 37680988 PMCID: PMC10480464 DOI: 10.1016/j.omtn.2023.08.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/16/2023] [Indexed: 09/09/2023]
Abstract
The recently discovered human lncRNA NORAD is induced after DNA damage in a p53-dependent manner. It plays a critical role in the maintenance of genomic stability through interaction with Pumilio proteins, limiting the repression of their target mRNAs. Therefore, NORAD inactivation causes chromosomal instability and aneuploidy, which contributes to the accumulation of genetic abnormalities and tumorigenesis. NORAD has been detected in several types of cancer, including breast cancer, which is the most frequently diagnosed and the second-leading cause of cancer death in women. In the present study, we confirmed upregulated NORAD expression levels in a set of human epithelial breast cancer cell lines (MDA-MB-231, MDA-MB-436, and MDA-MB-468), which belong to the most aggressive subtypes (triple-negative breast cancer). These results are in line with previous data showing that high NORAD expression levels in basal-like tumors were associated with poor prognosis. Here, we demonstrate that NORAD downregulation sensitizes triple-negative breast cancer cells to chemotherapy, through a potential accumulation of genomic aberrations and an impaired capacity to signal DNA damage. These results show that NORAD may represent an unexploited neoadjuvant therapeutic target for chemotherapy-unresponsive breast cancer.
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Affiliation(s)
- Catarina Alves-Vale
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
- Hospital CUF Descobertas, CUF Oncologia, 1998-018 Lisbon, Portugal
| | - Ana Maria Capela
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carlota Tavares-Marcos
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Beatriz Domingues-Silva
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Bruno Pereira
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP – Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Francisco Santos
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Carla Pereira Gomes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Guadalupe Espadas
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Rui Vitorino
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Eduard Sabidó
- Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Paula Borralho
- Hospital CUF Descobertas, CUF Oncologia, 1998-018 Lisbon, Portugal
- Faculdade de Medicina, Universidade de Lisboa, Av. Professor Egas Moniz, 1649-028 Lisboa, Portugal
| | - Sandrina Nóbrega-Pereira
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Bruno Bernardes de Jesus
- Department of Medical Sciences and Institute of Biomedicine – iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
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12
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Surendran H, Palaniyandi T, Natarajan S, Hari R, Viwanathan S, Baskar G, Abdul Wahab MR, Ravi M, Rajendran BK. Role of homeobox d10 gene targeted signaling pathways in cancers. Pathol Res Pract 2023; 248:154643. [PMID: 37406379 DOI: 10.1016/j.prp.2023.154643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/07/2023]
Abstract
Homeobox D10 (HOXD10) is a transcription factor from the homeobox gene family that controls cell differentiation and morphogenesis throughout development.Due to their functional interaction, changes in HOXD10 gene expression might induce tumors. This narrative review focuses on how and why the dysregulation in the signaling pathways linked with HOXD10 contributes to the metastatic development of cancer. Organ development and tissue homeostasis need highly conserved homeotic transcription factors from homeobox (HOX) genes. Their dysregulation disrupts regulatory molecule action, causing tumors. The HOXD10 gene is upregulated in breast, gastric, hepatocellular, colorectal, bladder, cholangiocellular carcinoma and prostate cancer. Tumor signaling pathways are affected by HOXD10 gene expression changes. This study examines HOXD10-associated signaling pathway dysregulation, which may alter metastatic cancer signaling. In addition, the theoretical foundations that alter HOXD10-mediated therapeutic resistance in malignancies has been presented. New cancer therapy methods will be simpler to develop with the newly discovered knowledge. This review showed that HOXD10 may be a tumor suppressor gene and a new cancer treatment target signaling pathway.
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Affiliation(s)
- Hemapreethi Surendran
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Deemed to be University, Chennai 600095 Tamil Nadu, India
| | - Thirunavukkarasu Palaniyandi
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Deemed to be University, Chennai 600095 Tamil Nadu, India; Department of Anatomy, Biomedical Research Unit and Laboratory Animal Centre, Saveetha Dental College and Hospital, SIMATS, Saveetha University, Chennai, Tamilnadu, India.
| | - Sudhakar Natarajan
- Department of Virology and Biotechnology, ICMR - National institute for Research in Tuberculosis (NIRT), Chetpet, Chennai 600031 Tamil Nadu, India
| | - Rajeswary Hari
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Deemed to be University, Chennai 600095 Tamil Nadu, India
| | - Sandhiya Viwanathan
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Deemed to be University, Chennai 600095 Tamil Nadu, India
| | - Gomathy Baskar
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Deemed to be University, Chennai 600095 Tamil Nadu, India
| | - Mugip Rahaman Abdul Wahab
- Department of Biotechnology, Dr. M.G.R Educational and Research Institute, Deemed to be University, Chennai 600095 Tamil Nadu, India
| | - Maddaly Ravi
- Department of Human Genetics, Sri Ramachandra Institute of Higher Education and Research, Chennai 600116 Tamil Nadu, India
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13
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Aba PE, Ihedioha JI, Asuzu IU. A review of the mechanisms of anti-cancer activities of some medicinal plants-biochemical perspectives. J Basic Clin Physiol Pharmacol 2023; 34:419-428. [PMID: 34936737 DOI: 10.1515/jbcpp-2021-0257] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/28/2021] [Indexed: 06/14/2023]
Abstract
Cancer is a disease resulting in unbridled growth of cells due to dysregulation in the balance of cell populations. Various management procedures in handling cases of cancer are not without their adverse side effects on the normal cells. Medicinal plants/herbs have been in use in the management of various ailments, including cancer, for a long time. Medicinal plants have been credited with wide safety margins, cost effectiveness, availability and diverse activities. This study reviewed various mechanisms of anti-cancer activities of some medicinal plants from a biochemical perspective. The mechanisms of anti-cancer activities of plant compounds addressed in this article include induction of apoptosis, anti-angiogenic effects, anti-metastasis, inhibition of cell cycle, inhibition of DNA destruction and effects on key enzymes, cytotoxic and anti-oxidant effects. The anti-cancer activities of some of the plants involve more than one mechanism.
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Affiliation(s)
- Patrick E Aba
- Department of Veterinary Physiology and Pharmacology, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - John I Ihedioha
- Department of Veterinary Pathology and Microbiology, University of Nigeria, Nsukka, Enugu State, Nigeria
| | - Isaac U Asuzu
- Department of Veterinary Physiology and Pharmacology, University of Nigeria, Nsukka, Enugu State, Nigeria
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14
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Fatima GN, Fatma H, Saraf SK. Vaccines in Breast Cancer: Challenges and Breakthroughs. Diagnostics (Basel) 2023; 13:2175. [PMID: 37443570 DOI: 10.3390/diagnostics13132175] [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: 04/17/2023] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Breast cancer is a problem for women's health globally. Early detection techniques come in a variety of forms ranging from local to systemic and from non-invasive to invasive. The treatment of cancer has always been challenging despite the availability of a wide range of therapeutics. This is either due to the variable behaviour and heterogeneity of the proliferating cells and/or the individual's response towards the treatment applied. However, advancements in cancer biology and scientific technology have changed the course of the cancer treatment approach. This current review briefly encompasses the diagnostics, the latest and most recent breakthrough strategies and challenges, and the limitations in fighting breast cancer, emphasising the development of breast cancer vaccines. It also includes the filed/granted patents referring to the same aspects.
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Affiliation(s)
- Gul Naz Fatima
- Division of Pharmaceutical Chemistry, Faculty of Pharmacy, Babu Banarasi Das Northern India Institute of Technology, Lucknow 226028, Uttar Pradesh, India
| | - Hera Fatma
- Division of Pharmaceutical Chemistry, Faculty of Pharmacy, Babu Banarasi Das Northern India Institute of Technology, Lucknow 226028, Uttar Pradesh, India
| | - Shailendra K Saraf
- Division of Pharmaceutical Chemistry, Faculty of Pharmacy, Babu Banarasi Das Northern India Institute of Technology, Lucknow 226028, Uttar Pradesh, India
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15
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Debbarma A, Mansolf M, Khatri VA, Valentino JA, Sapi E. Effect of Borrelia burgdorferi on the Expression of miRNAs in Breast Cancer and Normal Mammary Epithelial Cells. Microorganisms 2023; 11:1475. [PMID: 37374977 DOI: 10.3390/microorganisms11061475] [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: 05/12/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer is one of the leading causes of death in women worldwide. Recent studies have demonstrated that inflammation due to infections with microorganisms could play a role in breast cancer development. One of the known human pathogens, Borrelia burgdorferi, the causative agent of Lyme disease, has been shown to be present in various types of breast cancer and is associated with poor prognosis. We reported that B. burgdorferi can invade breast cancer cells and affect their tumorigenic phenotype. To better understand the genome-wide genetic changes caused by B. burgdorferi, we evaluated the microRNA (miRNA or miR) expression profiles of two triple-negative breast cancer cell lines and one non-tumorigenic mammary cell line before and after B. burgdorferi infection. Using a cancer-specific miRNA panel, four miRNAs (miR-206, 214-3p, 16-5p, and 20b-5p) were identified as potential markers for Borrelia-induced changes, and the results were confirmed by quantitative real-time reverse transcription (qRT-PCR). Among those miRNAs, miR-206 and 214 were the most significantly upregulated miRNAs. The cellular impact of miR-206 and 214 was evaluated using DIANA software to identify related molecular pathways and genes. Analyses showed that the cell cycle, checkpoints, DNA damage-repair, proto-oncogenes, and cancer-related signaling pathways are mostly affected by B. burgdorferi infection. Based on this information, we have identified potential miRNAs which could be further evaluated as biomarkers for tumorigenesis caused by pathogens in breast cancer cells.
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Affiliation(s)
- Ananya Debbarma
- Lyme Disease Research Group, Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Road, West Haven, CT 06516, USA
| | - Miranda Mansolf
- Lyme Disease Research Group, Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Road, West Haven, CT 06516, USA
| | - Vishwa A Khatri
- Lyme Disease Research Group, Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Road, West Haven, CT 06516, USA
| | - Justine A Valentino
- Lyme Disease Research Group, Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Road, West Haven, CT 06516, USA
| | - Eva Sapi
- Lyme Disease Research Group, Department of Biology and Environmental Science, University of New Haven, 300 Boston Post Road, West Haven, CT 06516, USA
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16
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Shomali N, Kamrani A, Heris JA, Shahabi P, Nasiri H, Sadeghvand S, Ghahremanzadeh K, Akbari M. Dysregulation of P53 in breast cancer: Causative factors and treatment strategies. Pathol Res Pract 2023; 247:154539. [PMID: 37257244 DOI: 10.1016/j.prp.2023.154539] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 06/02/2023]
Abstract
One of the most prevalent cancers impacting women worldwide is breast cancer. Although there are several risk factors for breast cancer, the p53 gene's function has recently received much attention. The "gatekeeper" gene, or p53, is sometimes referred to as such since it is crucial in controlling cell proliferation and preventing the development of malignant cells. By identifying DNA damage and initiating cellular repair processes, p53 usually functions as a tumor-suppressor. But p53 gene alterations can result in a lack of function, allowing cells to divide out of control and perhaps triggering the onset of cancer. Various factors, such as mutation genes, signaling pathways, and hormones, can dysregulate P53 proteins and cause breast cancer. A promising strategy for individualized cancer treatment involves focusing on p53 mutations in breast cancer. While numerous techniques, including gene therapy and small compounds, have shown promise, further study is required to create safe and efficient treatments to target p53 mutations in breast cancer successfully.
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Affiliation(s)
- Navid Shomali
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran
| | - Amin Kamrani
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Science, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javad Ahmadian Heris
- Department of Allergy and Clinical Immunology, Pediatric Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Parviz Shahabi
- Department of Physiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran; Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hadi Nasiri
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Shahram Sadeghvand
- Pediatrics Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | | | - Morteza Akbari
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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17
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Demirel D, Ozkaya FC, Ebrahim W, Sokullu E, Sahin ID. Aspergillus Carneus metabolite Averufanin induced cell cycle arrest and apoptotic cell death on cancer cell lines via inducing DNA damage. Sci Rep 2023; 13:6460. [PMID: 37081051 PMCID: PMC10119153 DOI: 10.1038/s41598-023-30775-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/28/2023] [Indexed: 04/22/2023] Open
Abstract
Cancer is one of the leading causes of death worldwide, accounting for nearly 10 million deaths in 2020. Current treatment methods include hormone therapy, γ-radiation, immunotherapy, and chemotherapy. Although chemotherapy is the most effective treatment, there are major obstacles posed by resistance mechanisms of cancer cells and side-effects of the drugs, thus the search for novel anti-cancer compounds, especially from natural sources, is crucial for cancer pharmaceutics research. One natural source worthy of investigation is fungal species. In this study, the cytotoxicity of 5 metabolic compounds isolated from filamentous fungus Aspergillus Carneus. Arugosin C, Averufin, Averufanin, Nidurifin and Versicolorin C were analyzed using NCI-SRB assay on 10 different cell lines of breast cancer, ovarian cancer, glioblastoma and non-tumorigenic cell lines. Averufanin showed highest cytotoxicity with lowest IC50 concentrations especially on breast cancer cells. Therefore, Averufanin was further investigated to enlighten cell death and molecular mechanisms of action involved. Cell cycle analysis showed increase in SubG1 phase suggesting apoptosis induction which was further confirmed by Annexin V and Caspase 3/7 Assays. H2A.X staining revealed accumulation of DNA damage in cells treated with Averufanin and finally western blot analysis validated DNA damage response and downstream effects of Averufanin treatment in various signaling pathways. Consequently, this study shows that Averufanin compound induces cell cycle arrest and cell death via apoptosis through causing DNA damage and can be contemplated and further explored as a new therapeutic strategy in breast cancer.
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Affiliation(s)
- Deren Demirel
- Koc University Research Center for Translational Medicine (KUTTAM), Sariyer, Istanbul, Turkey
| | - Ferhat Can Ozkaya
- Aliaga Industrial Zone Technology Transfer Office, Aliaga, 35800, İzmir, Turkey
| | - Weaam Ebrahim
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt
| | - Emel Sokullu
- Koc University Research Center for Translational Medicine (KUTTAM), Sariyer, Istanbul, Turkey.
- Koc University, School of Medicine, Sariyer, 34450, Istanbul, Turkey.
| | - Irem Durmaz Sahin
- Koc University Research Center for Translational Medicine (KUTTAM), Sariyer, Istanbul, Turkey.
- Koc University, School of Medicine, Sariyer, 34450, Istanbul, Turkey.
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18
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Yin JY, Lu XT, Hou ML, Cao T, Tian Z. Sirtuin1-p53: a potential axis for cancer therapy. Biochem Pharmacol 2023; 212:115543. [PMID: 37037265 DOI: 10.1016/j.bcp.2023.115543] [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: 11/26/2022] [Revised: 03/31/2023] [Accepted: 04/03/2023] [Indexed: 04/12/2023]
Abstract
Sirtuin1 (SIRT1) is a conserved nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylase that plays key roles in a range of cellular events, including the maintenance of genome stability, gene regulation, cell proliferation, and apoptosis. P53 is one of the most studied tumor suppressors and the first identified non-histone target of SIRT1. SIRT1 deacetylates p53 in a NAD+-dependent manner and inhibits its transcriptional activity, thus exerting action on a series of pathways related to tissue homeostasis and various pathological states. The SIRT1-p53 axis is thought to play a central role in tumorigenesis. Although SIRT1 was initially identified as a tumor promoter, evidence now indicates that SIRT1 may also act as a tumor suppressor. This seemingly contradictory evidence indicates that the functionality of SIRT1 may be dictated by different cell types and intracellular localization patterns. In this review, we summarize recent evidence relating to the interactions between SIRT1 and p53 and discuss the relative roles of these two molecules with regards to cancer-associated cellular events. We also provide an overview of current knowledge of SIRT1-p53 signaling in tumorigenesis. Given the vital role of the SIRT1-p53 pathway, targeting this axis may provide promising strategies for the treatment of cancer.
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Affiliation(s)
- Jia-Yi Yin
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Xin-Tong Lu
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Meng-Ling Hou
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Ting Cao
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China
| | - Zhen Tian
- College of Pharmaceutical Sciences, Southwest University, Chongqing, China.
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19
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Amini P, Hajihosseini M, Pyne S, Dinu I. Geographically weighted linear combination test for gene-set analysis of a continuous spatial phenotype as applied to intratumor heterogeneity. Front Cell Dev Biol 2023; 11:1065586. [PMID: 36998245 PMCID: PMC10044624 DOI: 10.3389/fcell.2023.1065586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/22/2023] [Indexed: 03/11/2023] Open
Abstract
Background: The impact of gene-sets on a spatial phenotype is not necessarily uniform across different locations of cancer tissue. This study introduces a computational platform, GWLCT, for combining gene set analysis with spatial data modeling to provide a new statistical test for location-specific association of phenotypes and molecular pathways in spatial single-cell RNA-seq data collected from an input tumor sample.Methods: The main advantage of GWLCT consists of an analysis beyond global significance, allowing the association between the gene-set and the phenotype to vary across the tumor space. At each location, the most significant linear combination is found using a geographically weighted shrunken covariance matrix and kernel function. Whether a fixed or adaptive bandwidth is determined based on a cross-validation cross procedure. Our proposed method is compared to the global version of linear combination test (LCT), bulk and random-forest based gene-set enrichment analyses using data created by the Visium Spatial Gene Expression technique on an invasive breast cancer tissue sample, as well as 144 different simulation scenarios.Results: In an illustrative example, the new geographically weighted linear combination test, GWLCT, identifies the cancer hallmark gene-sets that are significantly associated at each location with the five spatially continuous phenotypic contexts in the tumors defined by different well-known markers of cancer-associated fibroblasts. Scan statistics revealed clustering in the number of significant gene-sets. A spatial heatmap of combined significance over all selected gene-sets is also produced. Extensive simulation studies demonstrate that our proposed approach outperforms other methods in the considered scenarios, especially when the spatial association increases.Conclusion: Our proposed approach considers the spatial covariance of gene expression to detect the most significant gene-sets affecting a continuous phenotype. It reveals spatially detailed information in tissue space and can thus play a key role in understanding the contextual heterogeneity of cancer cells.
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Affiliation(s)
- Payam Amini
- Department of Biostatistics, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
- School of Medicine, Keele University, Keele, Staffordshire, United Kingdom
| | - Morteza Hajihosseini
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- Stanford Department of Urology, Center for Academic Medicine, Palo Alto, CA, United States
| | - Saumyadipta Pyne
- Health Analytics Network, Pittsburgh, PA, United States
- University of California, Santa Barbara, Santa Barbara, CA, United States
- *Correspondence: Saumyadipta Pyne, ; Irina Dinu,
| | - Irina Dinu
- School of Public Health, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Saumyadipta Pyne, ; Irina Dinu,
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20
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Steffens Reinhardt L, Groen K, Newton C, Avery-Kiejda KA. The role of truncated p53 isoforms in the DNA damage response. Biochim Biophys Acta Rev Cancer 2023; 1878:188882. [PMID: 36977456 DOI: 10.1016/j.bbcan.2023.188882] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/23/2023] [Accepted: 02/25/2023] [Indexed: 03/28/2023]
Abstract
The tumour suppressor p53 is activated following genotoxic stress and regulates the expression of target genes involved in the DNA damage response (DDR). The discovery that p53 isoforms alter the transcription of p53 target genes or p53 protein interactions unveiled an alternative DDR. This review will focus on the role p53 isoforms play in response to DNA damage. The expression of the C-terminally truncated p53 isoforms may be modulated via DNA damage-induced alternative splicing, whereas alternative translation plays an important role in modulating the expression of N-terminally truncated isoforms. The DDR induced by p53 isoforms may enhance the canonical p53 DDR or block cell death mechanisms in a DNA damage- and cell-specific manner, which could contribute to chemoresistance in a cancer context. Thus, a better understanding of the involvement of p53 isoforms in the cell fate decisions could uncover potential therapeutic targets in cancer and other diseases.
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Affiliation(s)
- Luiza Steffens Reinhardt
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, NSW, Australia; Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Kira Groen
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, NSW, Australia; Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Cheryl Newton
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, NSW, Australia; Hunter Medical Research Institute, Newcastle, NSW, Australia
| | - Kelly A Avery-Kiejda
- School of Biomedical Sciences and Pharmacy, College of Health, Medicine and Wellbeing, The University of Newcastle, Newcastle, NSW, Australia; Hunter Medical Research Institute, Newcastle, NSW, Australia.
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21
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Elson NC, Lewis JD, Shaughnessy EA, Reyna C. Lessons from other fields of medicine, Part 1: Breast cancer. HANDBOOK OF CLINICAL NEUROLOGY 2023; 192:101-118. [PMID: 36796936 DOI: 10.1016/b978-0-323-85538-9.00003-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Through the understanding of multiple etiologies, pathologies, and disease progression trajectories, breast cancer shifted historically from a singular malignancy of the breast to a complex of molecular/biological entities, translating into individualized disease-modifying treatments. As a result, this led to various de-escalations of treatment compared with the gold standard in the era preceding systems biology: radical mastectomy. Targeted therapies have minimized morbidity from the treatments and mortality from the disease. Biomarkers further individualized tumor genetics and molecular biology to optimize treatments targeting specific cancer cells. Landmark discoveries in breast cancer management have evolved through histology, hormone receptors, human epidermal growth factor, single-gene prognostic markers, and multigene prognostic markers. Relevant to the reliance on histopathology in neurodegenerative disorders, histopathology evaluation in breast cancer can serve as a marker of overall prognosis rather than predict response to therapies. This chapter reviews the successes and failures of breast cancer research through history, with focus on the transition from a universal approach for all patients to divergent biomarker development and individualized targeted therapies, discussing future areas of growth in the field that may apply to neurodegenerative disorders.
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Affiliation(s)
- Nora C Elson
- Department of Surgery, Good Samaritan TriHealth Hospitals, Cincinnati, OH, United States
| | - Jaime D Lewis
- Department of Surgery, University of Cincinnati Medical Center, Cincinnati, OH, United States
| | - Elizabeth A Shaughnessy
- Department of Surgery, University of Cincinnati Medical Center, Cincinnati, OH, United States
| | - Chantal Reyna
- Department of Surgery, Crozer Health Hospitals, Springfield, PA, United States.
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22
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Flores Fortis M, Perez Añorve IX, Del Moral Hernandez O, Villegas N, Arechaga Ocampo E. Transcriptomic profiles-based approach to decode the role of miR-122 in triple negative breast cancer. Genes Chromosomes Cancer 2023; 62:392-404. [PMID: 36695641 DOI: 10.1002/gcc.23126] [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: 09/24/2022] [Revised: 01/16/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023] Open
Abstract
miR-122 has been considered both as tumor suppressor miRNA and oncomiR in breast tumor phenotypes. However, the role of miR-122 in triple-negative breast cancer (TNBC) is still unknown. In this study, the clinical value of miR-122 was used to describe the transcriptomic landscape of TNBC tumors obtained from The Cancer Genome Atlas database. Low expression levels of miR-122 were associated with poor overall survival (OS) of TNBC patients than those with higher expression levels of miR-122. We identified gene expression profiles in TNBC tumors expressed lower or higher miR-122. Gene coexpression networks analysis revealed gene modules and hub genes specific to TNBC tumors with low or high miR-122 levels. Gene ontology and KEGG pathways analysis revealed that gene modules in TNBC with gain of miR-122 were related to cell cycle and DNA repair, while in TNBC with loss of miR-122 were enriched in cell cycle, proliferation, apoptosis and activation of cell migration and invasion. The expression of hub genes distinguished TNBC tumors with gain or loss of miR-122 from normal breast tissues. Furthermore, high levels of hub genes were associated with better OS in TNBC patients. Interestingly, the gene coexpression network related to loss of miR-122 were enriched with target genes of miR-122, but this did not observed in those with gain of miR-122. Target genes of miR-122 are oncogenes mainly associated with cell differentiation-related processes. Finally, 75 genes were identified exclusively associated to loss of miR-122, which are also implicated in cell differentiation. In conclusion, miR-122 could act as tumor suppressor by controlling oncogenes in TNBC.
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Affiliation(s)
- Mauricio Flores Fortis
- Posgrado en Ciencias Naturales e Ingenieria, Unidad Cuajimalpa, Universidad Autonoma Metropolitana, Mexico City, Mexico.,Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autonoma Metropolitana, Mexico City, Mexico
| | - Isidro X Perez Añorve
- Laboratorio de Patología Vascular Cerebral, Instituto Nacional de Neurologia y Neurocirugia Manuel Velasco Suarez, Mexico City, Mexico
| | - Oscar Del Moral Hernandez
- Laboratorio de Virologia, Facultad de Ciencias Quimico Biologicas, Universidad Autonoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - Nicolas Villegas
- Departamento de Biomedicina Molecular, Centro de Investigacion y de Estudios Avanzados (CINVESTAV), Mexico City, Mexico
| | - Elena Arechaga Ocampo
- Departamento de Ciencias Naturales, Unidad Cuajimalpa, Universidad Autonoma Metropolitana, Mexico City, Mexico
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23
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Khanal P, Patil VS, Bhandare VV, Patil PP, Patil BM, Dwivedi PSR, Bhattacharya K, Harish DR, Roy S. Systems and in vitro pharmacology profiling of diosgenin against breast cancer. Front Pharmacol 2023; 13:1052849. [PMID: 36686654 PMCID: PMC9846155 DOI: 10.3389/fphar.2022.1052849] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Aim: The purpose of this study was to establish a mode of action for diosgenin against breast cancer employing a range of system biology tools and to corroborate its results with experimental facts. Methodology: The diosgenin-regulated domains implicated in breast cancer were enriched in the Kyoto Encyclopedia of Genes and Genomes database to establish diosgenin-protein(s)-pathway(s) associations. Later, molecular docking and the lead complexes were considered for molecular dynamics simulations, MMPBSA, principal component, and dynamics cross-correlation matrix analysis using GROMACS v2021. Furthermore, survival analysis was carried out for the diosgenin-regulated proteins that were anticipated to be involved in breast cancer. For gene expression analyses, the top three targets with the highest binding affinity for diosgenin and tumor expression were examined. Furthermore, the effect of diosgenin on cell proliferation, cytotoxicity, and the partial Warburg effect was tested to validate the computational findings using functional outputs of the lead targets. Results: The protein-protein interaction had 57 edges, an average node degree of 5.43, and a p-value of 3.83e-14. Furthermore, enrichment analysis showed 36 KEGG pathways, 12 cellular components, 27 molecular functions, and 307 biological processes. In network analysis, three hub proteins were notably modulated: IGF1R, MDM2, and SRC, diosgenin with the highest binding affinity with IGF1R (binding energy -8.6 kcal/mol). Furthermore, during the 150 ns molecular dynamics (MD) projection run, diosgenin exhibited robust intermolecular interactions and had the least free binding energy with IGF1R (-35.143 kcal/mol) compared to MDM2 (-34.619 kcal/mol), and SRC (-17.944 kcal/mol). Diosgenin exhibited the highest cytotoxicity against MCF7 cell lines (IC50 12.05 ± 1.33) µg/ml. Furthermore, in H2O2-induced oxidative stress, the inhibitory constant (IC50 7.68 ± 0.51) µg/ml of diosgenin was lowest in MCF7 cell lines. However, the reversal of the Warburg effect by diosgenin seemed to be maximum in non-cancer Vero cell lines (EC50 15.27 ± 0.95) µg/ml compared to the rest. Furthermore, diosgenin inhibited cell proliferation in SKBR3 cell lines more though. Conclusion: The current study demonstrated that diosgenin impacts a series of signaling pathways, involved in the advancement of breast cancer, including FoxO, PI3K-Akt, p53, Ras, and MAPK signaling. Additionally, diosgenin established a persistent diosgenin-protein complex and had a significant binding affinity towards IGF1R, MDM2, and SRC. It is possible that this slowed down cell growth, countered the Warburg phenomenon, and showed the cytotoxicity towards breast cancer cells.
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Affiliation(s)
- Pukar Khanal
- Department of Pharmacology, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, India,*Correspondence: Pukar Khanal, ; Darasaguppe R. Harish,
| | - Vishal S. Patil
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
| | | | - Priyanka P. Patil
- Department of Pharmacology, KLE College of Pharmacy Belagavi, KLE Academy of Higher Education and Research (KAHER), Belagavi, India
| | - B. M. Patil
- PRES’s Pravara Rural College of Pharmacy Pravaranagar, Loni, Maharashtra, India
| | - Prarambh S. R. Dwivedi
- Department of Pharmacology, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, India
| | - Kunal Bhattacharya
- Pratiksha Institute of Pharmaceutical Sciences, Guwahati, Assam, India,Royal School of Pharmacy, The Assam Royal Global University, Guwahati, Assam, India
| | - Darasaguppe R. Harish
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India,*Correspondence: Pukar Khanal, ; Darasaguppe R. Harish,
| | - Subarna Roy
- ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
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24
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Zhu L, Liu K, Bao B, Li F, Liang W, Jiang Z, Hao X, Wang J. A nomogram based on genotypic and clinicopathologic factors to predict the non-sentinel lymph node metastasis in Chinese women breast cancer patients. Front Oncol 2023; 13:1028830. [PMID: 37152050 PMCID: PMC10154525 DOI: 10.3389/fonc.2023.1028830] [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: 08/26/2022] [Accepted: 03/29/2023] [Indexed: 05/09/2023] Open
Abstract
Background Sentinel lymph node biopsy (SLNB) is the standard treatment for breast cancer patients with clinically negative axilla. However, axillary lymph node dissection (ALND) is still the standard care for sentinel lymph node (SLN) positive patients. Clinical data reveals about 40-75% of patients without non-sentinel lymph node (NSLN) metastasis after ALND. Unnecessary ALND increases the risk of complications and detracts from quality of life. In this study, we expect to develop a nomogram based on genotypic and clinicopathologic factors to predict the risk of NSLN metastasis in SLN-positive Chinese women breast cancer patients. Methods This retrospective study collected data from 1,879 women breast cancer patients enrolled from multiple centers. Genotypic features contain 96 single nucleotide polymorphisms (SNPs) associated with breast cancer susceptibility, therapy and prognosis. SNP genotyping was identified by the quantitative PCR detection platform. The genetic features were divided into two clusters by the mutational stability. The normalized polygenic risk score (PRS) was used to evaluate the combined effect of each SNP cluster. Recursive feature elimination (RFE) based on linear discriminant analysis (LDA) was adopted to select the most useful predictive features, and RFE based on support vector machine (SVM) was used to reduce the number of SNPs. Multivariable logistic regression models (i.e., nomogram) were built for predicting NSLN metastasis. The predictive abilities of three types of model (based on only clinicopathologic information, the integrated clinicopathologic and all SNPs information, and integrated clinicopathologic and significant SNPs information) were compared. Internal and external validations were performed and the area under ROC curves (AUCs) as well as a series of evaluation indicators were assessed. Results 229 patients underwent SLNB followed by ALND and without any neo-adjuvant therapy, 79 among them (34%) had a positive axillary NSLN metastasis. The LDA-RFE identified the characteristics including lymphovascular invasion, number of positive SLNs, number of negative SLNs and two SNP clusters as significant predictors of NSLN metastasis. Furthermore, the SVM-RFE selected 29 significant SNPs in the prediction of NSLN metastasis. In internal validation, the median AUCs of the clinical and all SNPs combining model, the clinical and 29 significant SNPs combining model, and the clinical model were 0.837, 0.795 and 0.708 respectively. Meanwhile, in external validation, the AUCs of the three models were 0.817, 0.815 and 0.745 respectively. Conclusion We present a new nomogram by combining genotypic and clinicopathologic factors to achieve higher sensitivity and specificity comparing with traditional clinicopathologic factors to predict NSLN metastasis in Chinese women breast cancer. It is recommended that more validations are required in prospective studies among different patient populations.
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Affiliation(s)
- Liling Zhu
- Department of Breast Surgery, Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Liling Zhu, ; Xiaopeng Hao, ; Jiandong Wang,
| | - Ke Liu
- Academic Department of Breast Cancer Education Association, Beijing, China
| | - Baoshi Bao
- Department of General Surgery, The First Medical Center of the General Hospital of the People’s Liberation Army of China, Beijing, China
| | - Fengyun Li
- Academic Department of Breast Cancer Education Association, Beijing, China
| | - Wentao Liang
- Academic Department of Beijing Centragene Technology Co., Ltd., Beijing, China
| | - Zhaoyun Jiang
- Academic Department of Breast Cancer Education Association, Beijing, China
| | - Xiaopeng Hao
- Department of General Surgery, The First Medical Center of the General Hospital of the People’s Liberation Army of China, Beijing, China
- *Correspondence: Liling Zhu, ; Xiaopeng Hao, ; Jiandong Wang,
| | - Jiandong Wang
- Department of General Surgery, The First Medical Center of the General Hospital of the People’s Liberation Army of China, Beijing, China
- *Correspondence: Liling Zhu, ; Xiaopeng Hao, ; Jiandong Wang,
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25
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Patra D, Bhavya K, Ramprasad P, Kalia M, Pal D. Anti-cancer drug molecules targeting cancer cell cycle and proliferation. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:343-395. [PMID: 37061337 DOI: 10.1016/bs.apcsb.2022.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Cancer, a vicious clinical burden that potentiates maximum fatality for humankind, arises due to unregulated excessive cell division and proliferation through an eccentric expression of cell cycle regulator proteins. A set of evolutionarily conserved machinery controls the cell cycle in an extremely precise manner so that a cell that went through the cycle can produce a genetically identical copy. To achieve perfection, several checkpoints were placed in the cycle for surveillance; so, errors during the division were rectified by the repair strategies. However, irreparable damage leads to exit from the cell cycle and induces programmed cell death. In comparison to a normal cell, cancer cells facilitate the constitutive activation of many dormant proteins and impede negative regulators of the checkpoint. Extensive studies in the last few decades on cell division and proliferation of cancer cells elucidate the molecular mechanism of the cell-cycle regulators that are often targeted for the development of anti-cancer therapy. Each phase of the cell cycle has been regulated by a unique set of proteins including master regulators Cyclins, and CDKs, along with the accessory proteins such as CKI, Cdc25, error-responsive proteins, and various kinase proteins mainly WEE1 kinases, Polo-like kinases, and Aurora kinases that control cell division. Here in this chapter, we have analytically discussed the role of cell cycle regulators and proliferation factors in cancer progression and the rationale of using various cell cycle-targeting drug molecules as anti-cancer therapy.
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Affiliation(s)
- Debarun Patra
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Kumari Bhavya
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Palla Ramprasad
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Moyna Kalia
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Durba Pal
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India.
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26
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Halim F, Azhar Y, Suwarman S, Hernowo B. p53 Mutation as Plausible Predictor for Endocrine Resistance Therapy in Luminal Breast Cancer. F1000Res 2022; 11:330. [PMID: 36519010 PMCID: PMC9718986 DOI: 10.12688/f1000research.108628.2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/11/2022] [Indexed: 12/05/2022] Open
Abstract
Endocrine therapy resistance in Luminal Breast Cancer is a significant issue to be tackled, but currently, no specific biomarker could be used to anticipate this event. p53 mutation is widely known as one of Breast Cancer's most prominent genetic alterations. Its mutation could generate various effects in Estrogen Receptor and Progesterone Receptor molecular works, tangled in events leading to the aggravation of endocrine therapy resistance. Hence the possibility of p53 mutation utilization as an endocrine therapy resistance predictive biomarker is plausible. The purpose of this review is to explore the latest knowledge of p53 role in Estrogen Receptor and Progesterone Receptor molecular actions, thus aggravating the Endocrine Therapy resistance in Luminal Breast Cancer, from which we could define possibilities and limitations to utilize p53 as the predictive biomarker of endocrine therapy resistance in Luminal Breast Cancer.
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Affiliation(s)
- Freda Halim
- Department of Surgery, Pelita Harapan University, Tangerang, Indonesia,
| | - Yohana Azhar
- Department of Surgery - Oncology, Head and Neck Division, Hasan Sadikin General Hospital, Universitas Padjajaran, Bandung, Indonesia
| | - Suwarman Suwarman
- Department of Anesthesiology and Intensive Care, Hasan Sadikin General Hospital, Universitas Padjajaran, Bandung, Indonesia
| | - Bethy Hernowo
- Department of Anatomical Pathology, Universitas Padjajaran, Bandung, West Java, Indonesia
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27
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Alterations in the p53 isoform ratio govern breast cancer cell fate in response to DNA damage. Cell Death Dis 2022; 13:907. [PMID: 36307393 PMCID: PMC9616954 DOI: 10.1038/s41419-022-05349-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022]
Abstract
Our previous studies have shown that p53 isoform expression is altered in breast cancer and related to prognosis. In particular, a high ∆40p53:p53α ratio is associated with worse disease-free survival. In this manuscript, the influence of altered Δ40p53 and p53α levels on the response to standard of care DNA-damaging agents used in breast cancer treatment was investigated in vitro. Our results revealed that a high Δ40p53:p53α ratio causes cells to respond differently to doxorubicin and cisplatin treatments. Δ40p53 overexpression significantly impairs the cells' sensitivity to doxorubicin through reducing apoptosis and DNA damage, whereas Δ40p53 knockdown has the opposite effect. Further, a high Δ40p53:p53α ratio inhibited the differential expression of several genes following doxorubicin and promoted DNA repair, impairing the cells' canonical response. Overall, our results suggest that the response of breast cancer cells to standard of care DNA-damaging therapies is dependent on the expression of p53 isoforms, which may contribute to outcomes in breast cancer.
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28
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Minabian S, Soleimani S. S, Torabi M, Mohammadi M, Ranjbar H. Evaluation of P53 protein expression in gingival tissues of patients with chronic periodontitis by immunohistochemistry methods. Clin Exp Dent Res 2022; 8:1348-1353. [PMID: 36263737 PMCID: PMC9760160 DOI: 10.1002/cre2.668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 09/09/2022] [Accepted: 09/14/2022] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE Periodontitis is one of the most important periodontal diseases that can be affected by many factors. Although the mechanism of periodontitis development is not yet fully understood, previous studies suggest that apoptosis may be one of the pathological factors that can affect the process of the disease by destroying old and damaged cells. Low expression of P53 protein is one of the reasons for delaying cell death that allows damaged cells to survive longer and gives more time for the chance of mutations and pathogenesis. Because of the important role of P53 in gingival cells of patients with chronic periodontitis, the objective of our study is to evaluate the P53 protein expression in gingival tissues of patients with chronic periodontitis by immunohistochemistry methods. MATERIALS AND METHODS In this cross-sectional study, 35 patients with severe to moderate chronic periodontitis (loss of attachment ≥3 mm, probing depth ≥5 mm) with no treatment and 25 people who were healthy for periodontal problems were examined. Gingival biopsies from marginal and attached gingiva were obtained, prepared, and mounted on slides. Then, the expression of P53 on each slide was evaluated by optic microscopy after using P53 antibodies and staining with hematoxylin-eosin (immunohistochemistry method). Data were analyzed using independent t-test, Mann-Whitney U-test, and Spearman correlation test using SPSS Statistics version 18.0. RESULTS The mean ages of participants in the case and control groups were 37.58 and 32.09, respectively. Our results showed that the expression of P53 was not significant in periodontitis compared to the control group (p > .05). Also, gender could not affect the expression of P53 in both groups (p > .05), and there was no significant relationship between age and P53 gene incidence. CONCLUSION Chronic periodontitis has no significant effect on P53 expression, so changes in apoptosis due to P53 expression in periodontitis are not significant.
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Affiliation(s)
- Samaneh Minabian
- Oral and Dental Diseases Research CenterKerman University of Medical SciencesKermanIran
| | - Shima Soleimani S.
- Oral and Dental Diseases Research CenterKerman University of Medical SciencesKermanIran
| | - Molook Torabi
- Oral and Dental Diseases Research CenterKerman University of Medical SciencesKermanIran,Oral and Maxillofacial Pathology Department, School of DentistryKerman University of Medical SciencesKermanIran
| | - Mohammad Mohammadi
- Oral and Dental Diseases Research CenterKerman University of Medical SciencesKermanIran,Periodontics Department, School of DentistryKerman University of Medical SciencesKermanIran
| | - Hadi Ranjbar
- Mental Health Research Center, Psychological Health Research InstituteIran University of Medical SciencesTehranIran
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Li J, Zhang H, Gao F. Identification of miRNA biomarkers for breast cancer by combining ensemble regularized multinomial logistic regression and Cox regression. BMC Bioinformatics 2022; 23:434. [PMID: 36258162 PMCID: PMC9580207 DOI: 10.1186/s12859-022-04982-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Breast cancer is one of the most common cancers in women. It is necessary to classify breast cancer subtypes because different subtypes need specific treatment. Identifying biomarkers and classifying breast cancer subtypes is essential for developing appropriate treatment methods for patients. MiRNAs can be easily detected in tumor biopsy and play an inhibitory or promoting role in breast cancer, which are considered promising biomarkers for distinguishing subtypes. RESULTS A new method combing ensemble regularized multinomial logistic regression and Cox regression was proposed for identifying miRNA biomarkers in breast cancer. After adopting stratified sampling and bootstrap sampling, the most suitable sample subset for miRNA feature screening was determined via ensemble 100 regularized multinomial logistic regression models. 124 miRNAs that participated in the classification of at least 3 subtypes and appeared at least 50 times in 100 integrations were screened as features. 22 miRNAs from the proposed feature set were further identified as the biomarkers for breast cancer by using Cox regression based on survival analysis. The accuracy of 5 methods on the proposed feature set was significantly higher than on the other two feature sets. The results of 7 biological analyses illustrated the rationality of the identified biomarkers. CONCLUSIONS The screened features can better distinguish breast cancer subtypes. Notably, the genes and proteins related to the proposed 22 miRNAs were considered oncogenes or inhibitors of breast cancer. 9 of the 22 miRNAs have been proved to be markers of breast cancer. Therefore, our results can be considered in future related research.
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Affiliation(s)
- Juntao Li
- College of Mathematics and Information Science, Henan Normal University, Xinxiang, China
| | - Hongmei Zhang
- College of Mathematics and Information Science, Henan Normal University, Xinxiang, China.
| | - Fugen Gao
- College of Mathematics and Information Science, Henan Normal University, Xinxiang, China
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30
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The Effect of Aflatoxin B1 on Tumor-Related Genes and Phenotypic Characters of MCF7 and MCF10A Cells. Int J Mol Sci 2022; 23:ijms231911856. [PMID: 36233156 PMCID: PMC9570345 DOI: 10.3390/ijms231911856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/13/2022] [Accepted: 09/17/2022] [Indexed: 11/21/2022] Open
Abstract
The fungal toxin aflatoxin B1 (AB1) and its reactive intermediate, aflatoxin B1-8, 9 epoxide, could cause liver cancer by inducing DNA adducts. AB1 exposure can induce changes in the expression of several cancer-related genes. In this study, the effect of AB1 exposure on breast cancer MCF7 and normal breast MCF10A cell lines at the phenotypic and epigenetic levels was investigated to evaluate its potential in increasing the risk of breast cancer development. We hypothesized that, even at low concentrations, AB1 can cause changes in the expression of important genes involved in four pathways, i.e., p53, cancer, cell cycle, and apoptosis. The transcriptomic levels of BRCA1, BRCA2, p53, HER1, HER2, cMyc, BCL2, MCL1, CCND1, WNT3A, MAPK1, MAPK3, DAPK1, Casp8, and Casp9 were determined in MCF7 and MCF10A cells. Our results illustrate that treating both cells with AB1 induced cytotoxicity and apoptosis with reduction in cell viability in a concentration-dependent manner. Additionally, AB1 reduced reactive oxygen species levels. Phenotypically, AB1 caused cell-cycle arrest at G1, hypertrophy, and increased cell migration rates. There were changes in the expression levels of several tumor-related genes, which are known to contribute to activating cancer pathways. The effects of AB1 on the phenotype and epigenetics of both MCF7 and MCF10A cells associated with cancer development observed in this study suggest that AB1 is a potential risk factor for developing breast cancer.
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Sarhangi N, Hajjari S, Heydari SF, Ganjizadeh M, Rouhollah F, Hasanzad M. Breast cancer in the era of precision medicine. Mol Biol Rep 2022; 49:10023-10037. [PMID: 35733061 DOI: 10.1007/s11033-022-07571-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 05/01/2022] [Accepted: 05/05/2022] [Indexed: 01/02/2023]
Abstract
Breast cancer is a heterogeneous disorder with different molecular subtypes and biological characteristics for which there are diverse therapeutic approaches and clinical outcomes specific to any molecular subtype. It is a global health concern due to a lack of efficient therapy regimens that might be used for all disease subtypes. Therefore, treatment customization for each patient depending on molecular characteristics should be considered. Precision medicine for breast cancer is an approach to diagnosis, treatment, and prevention of the disease that takes into consideration the patient's genetic makeup. Precision medicine provides the promise of highly individualized treatment, in which each individual breast cancer patient receives the most appropriate diagnostics and targeted therapies based on the genetic profile of cancer. The knowledge about the molecular features and development of breast cancer treatment approaches has increased, which led to the development of new targeted therapeutics. Tumor genomic profiling is the standard of care for breast cancer that could contribute to taking steps to better management of malignancies. It holds great promise for accurate prognostication, prediction of response to common systemic therapies, and individualized monitoring of the disease. The emergence of targeted treatment has significantly enhanced the survival of patients with breast cancer and contributed to reducing the economic costs of the health system. In this review, we summarized the therapeutic approaches associated with the molecular classification of breast cancer to help the best treatment selection specific to the target patient.
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Affiliation(s)
- Negar Sarhangi
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahrzad Hajjari
- Medical Genomics Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Seyede Fatemeh Heydari
- Medical Genomics Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Maryam Ganjizadeh
- Medical Genomics Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Fatemeh Rouhollah
- Medical Genomics Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mandana Hasanzad
- Personalized Medicine Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran. .,Medical Genomics Research Center, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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32
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Jayathirtha M, Neagu AN, Whitham D, Alwine S, Darie CC. Investigation of the effects of overexpression of jumping translocation breakpoint (JTB) protein in MCF7 cells for potential use as a biomarker in breast cancer. Am J Cancer Res 2022; 12:1784-1823. [PMID: 35530281 PMCID: PMC9077082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023] Open
Abstract
Jumping translocation breakpoint (JTB) gene acts as a tumor suppressor or an oncogene in different malignancies, including breast cancer (BC), where it was reported as overexpressed. However, the molecular functions, biological processes and underlying mechanisms through which JTB protein causes increased cell growth, proliferation and invasion is still not fully deciphered. Our goal is to identify the functions of JTB protein by cellular proteomics approaches. MCF7 breast cancer cells were transfected with sense orientation of hJTB cDNA in HA, His and FLAG tagged CMV expression vector to overexpress hJTB and the expression levels were confirmed by Western blotting (WB). Proteins extracted from transfected cells were separated by SDS-PAGE and the in-gel digested peptides were analyzed by nano-liquid chromatography tandem mass spectrometry (nanoLC-MS/MS). By comparing the proteome of cells with upregulated conditions of JTB vs control and identifying the protein dysregulation patterns, we aim to understand the function of this protein and its contribution to tumorigenesis. Gene Set Enrichment Analysis (GSEA) algorithm was performed to investigate the biological processes and pathways that are associated with the JTB protein upregulation. The results demonstrated four significantly enriched gene sets from the following significantly upregulated pathways: mitotic spindle assembly, estrogen response late, epithelial-to-mesenchymal transition (EMT) and estrogen response early. JTB protein itself is involved in mitotic spindle pathway by its role in cell division/cytokinesis, and within estrogen response early and late pathways, contributing to discrimination between luminal and mesenchymal breast cancer. Thus, the overexpressed JTB condition was significantly associated with an increased expression of ACTNs, FLNA, FLNB, EZR, MYOF, COL3A1, COL11A1, HSPA1A, HSP90A, WDR, EPPK1, FASN and FOXA1 proteins related to deregulation of cytoskeletal organization and biogenesis, mitotic spindle organization, ECM remodeling, cellular response to estrogen, proliferation, migration, metastasis, increased lipid biogenesis, endocrine therapy resistance, antiapoptosis and discrimination between different breast cancer subtypes. Other upregulated proteins for overexpressed JTB condition are involved in multiple cellular functions and pathways that become dysregulated, such as tumor microenvironment (TME) acidification, the transmembrane transport pathways, glycolytic flux, iron metabolism and oxidative stress, metabolic reprogramming, nucleocytosolic mRNA transport, transcriptional activation, chromatin remodeling, modulation of cell death pathways, stress responsive pathways, and cancer drug resistance. The downregulated proteins for overexpressed JTB condition are involved in adaptive communication between external and internal environment of cells and maintenance between pro-apoptotic and anti-apoptotic signaling pathways, vesicle trafficking and secretion, DNA lesions repair and suppression of genes involved in tumor progression, proteostasis, redox state regulation, biosynthesis of macromolecules, lipolytic pathway, carbohydrate metabolism, dysregulation of ubiquitin-mediated degradation system, cancer cell immune escape, cell-to-cell and cell-to-ECM interactions, and cytoskeletal behaviour. There were no significantly enriched downregulated pathways.
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Affiliation(s)
- Madhuri Jayathirtha
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of IasiCarol I Bvd. No. 22, Iasi 700505, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Shelby Alwine
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
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Elwakeel A. Abrogating the Interaction Between p53 and Mortalin (Grp75/HSPA9/mtHsp70) for Cancer Therapy: The Story so far. Front Cell Dev Biol 2022; 10:879632. [PMID: 35493098 PMCID: PMC9047732 DOI: 10.3389/fcell.2022.879632] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/15/2022] [Indexed: 11/22/2022] Open
Abstract
p53 is a transcription factor that activates the expression of a set of genes that serve as a critical barrier to oncogenesis. Inactivation of p53 is the most common characteristic in sporadic human cancers. Mortalin is a differentially sub-cellularly localized member of the heat shock protein 70 family of chaperones that has essential mitochondrial and extra-mitochondrial functions. Elevated mortalin levels in multiple cancerous tissues and tumor-derived cell lines emphasized its key role in oncogenesis. One of mortalin’s major oncogenic roles is the inactivation of p53. Mortalin binds to p53 sequestering it in the cytoplasm. Hence, p53 cannot freely shuttle to the nucleus to perform its tumor suppressor functions as a transcription factor. This protein-protein interaction was reported to be cancer-specific, hence, a selective druggable target for a rationalistic cancer therapeutic strategy. In this review article, the chronological identification of mortalin-p53 interactions is summarized, the challenges and general strategies for targeting protein-protein interactions are briefly discussed, and information about compounds that have been reported to abrogate mortalin-p53 interaction is provided. Finally, the reasons why the disruption of this druggable interaction has not yet been applied clinically are discussed.
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Wang Y, Zhang L, Shi G, Liu M, Zhao W, Zhang Y, Wang Y, Zhang N. Effects of Inflammatory Response Genes on the Immune Microenvironment in Colorectal Cancer. Front Genet 2022; 13:886949. [PMID: 35464849 PMCID: PMC9032353 DOI: 10.3389/fgene.2022.886949] [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: 03/01/2022] [Accepted: 03/14/2022] [Indexed: 11/13/2022] Open
Abstract
Background: The close relationship between colorectal cancer and inflammation has been widely reported. However, the relationship between colorectal cancer and inflammation at the genetic level is not fully understood.Method: From a genetic perspective, this study explored the relationship between inflammation-related genes and the immune microenvironment in colorectal cancer. We identified prognostic genes, namely CX3CL1, CCL22, SERPINE1, LTB4R, XCL1, GAL, TIMP1, ADIPOQ, and CRH, by using univariate and multivariate regression analyses. A risk scoring model for inflammatory response was established, and patients in The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database were divided into two groups: high risk group and low risk group.Results: The analysis showed that the prognosis of the two groups was significantly different, and the low-risk group had a higher survival rate and longer survival time. Pathways related to apoptosis, inflammatory response, and hypoxia were significantly enriched as shown via Gene Set Enrichment Analysis (GSEA). Activated dendritic cell infiltration was found in both the TCGA and GEO databases, and the CCL21 gene played a significant role in the process of activated dendritic cell infiltration. CCL21 gene was also positively correlated with inflammatory response, and the gene expression and risk score were significantly different between the two groups.Conclusion: In summary, inflammatory response has a direct impact on patients with colorectal cancer in the prognosis and immune infiltration and further research studies on the inflammatory response can help in advancing the development of immunotherapy for colorectal cancer.
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Affiliation(s)
| | | | | | | | | | | | - Ying Wang
- *Correspondence: Ying Wang, ; Nan Zhang,
| | - Nan Zhang
- *Correspondence: Ying Wang, ; Nan Zhang,
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Pashaei-Asl R, Pashaiasl M, Ebrahimie E, Lale Ataei M, Paknejad M. Apoptotic effects of human amniotic fluid mesenchymal stem cells conditioned medium on human MCF-7 breast cancer cell line. BIOIMPACTS : BI 2022; 13:191-206. [PMID: 37431479 PMCID: PMC10329748 DOI: 10.34172/bi.2022.23813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 07/12/2021] [Accepted: 08/04/2021] [Indexed: 07/12/2023]
Abstract
Introduction Breast cancer, as the most common malignancy among women, is shown to have a high mortality rate and resistance to chemotherapy. Research has shown the possible inhibitory role of Mesenchymal stem cells in curing cancer. Thus, the present work used human amniotic fluid mesenchymal stem cell-conditioned medium (hAFMSCs-CM) as an apoptotic reagent on the human MCF-7 breast cancer cell line. Methods Conditioned medium (CM) was prepared from hAFMSCs. After treating MCF-7 cells with CM, a number of analytical procedures (MTT, real-time PCR, western blot, and flow cytometry) were recruited to evaluate the cell viability, Bax and Bcl-2 gene expression, P53 protein expression, and apoptosis, respectively. Human fibroblast cells (Hu02) were used as the negative control. In addition, an integrated approach to meta-analysis was performed. Results The MCF-7 cells' viability was decreased significantly after 24 hours (P < 0.0001) and 72 hours (P < 0.05) of treatment. Compared with the control cells, Bax gene's mRNA expression increased and Bcl-2's mRNA expression decreased considerably after treating for 24 hours with 80% hAFMSCs-CM (P = 0.0012, P < 0.0001, respectively); an increasing pattern in P53 protein expression could also be observed. The flow cytometry analysis indicated apoptosis. Results from literature mining and the integrated meta-analysis showed that hAFMSCs-CM is able to activate a molecular network where Bcl2 downregulation stands in harmony with the upregulation of P53, EIF5A, DDB2, and Bax, leading to the activation of apoptosis. Conclusion Our finding demonstrated that hAFMSCs-CM presents apoptotic effect on MCF-7 cells; therefore, the application of hAFMSCs-CM, as a therapeutic reagent, can suppress breast cancer cells' viabilities and induce apoptosis.
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Affiliation(s)
- Roghiyeh Pashaei-Asl
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Pashaiasl
- Department of Anatomical Sciences, School of Medicine, Tabriz University of Medical Sciences
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Reproductive Biology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Maryam Lale Ataei
- Department of Anatomical Sciences, School of Medicine, Tabriz University of Medical Sciences
| | - Maliheh Paknejad
- Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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Yao K, Schaafsma E, Zhang B, Cheng C. Tumor cell intrinsic and extrinsic features predict prognosis in estrogen receptor positive breast cancer. PLoS Comput Biol 2022; 18:e1009495. [PMID: 35263321 PMCID: PMC8936467 DOI: 10.1371/journal.pcbi.1009495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/21/2022] [Accepted: 02/17/2022] [Indexed: 11/19/2022] Open
Abstract
Although estrogen-receptor-positive (ER+) breast cancer is generally associated with favorable prognosis, clinical outcome varies substantially among patients. Genomic assays have been developed and applied to predict patient prognosis for personalized treatment. We hypothesize that the recurrence risk of ER+ breast cancer patients is determined by both genomic mutations intrinsic to tumor cells and extrinsic immunological features in the tumor microenvironment. Based on the Cancer Genome Atlas (TCGA) breast cancer data, we identified the 72 most common genomic aberrations (including gene mutations and indels) in ER+ breast cancer and defined sample-specific scores that systematically characterized the deregulated pathways intrinsic to tumor cells. To further consider tumor cell extrinsic features, we calculated immune infiltration scores for six major immune cell types. Many individual intrinsic features are predictive of patient prognosis in ER+ breast cancer, and some of them achieved comparable accuracy with the Oncotype DX assay. In addition, statistical learning models that integrated these features predicts the recurrence risk of patients with significantly better performance than the Oncotype DX assay (our optimized random forest model AUC = 0.841, Oncotype DX model AUC = 0.792, p = 0.04). As a proof-of-concept, our study indicates the great potential of genomic and immunological features in prognostic prediction for improving breast cancer precision medicine. The framework introduced in this work can be readily applied to other cancers.
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Affiliation(s)
- Kevin Yao
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Evelien Schaafsma
- Department of Molecular and Systems Biology, Dartmouth College, Lebanon, New Hampshire, United States of America
- Department of Biomedical Data Science, The Geisel School of Medicine at Dartmouth College, Lebanon, New Hampshire, United States of America
| | - Baoyi Zhang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas, United States of America
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas, United States of America
- Institute for Clinical and Transcriptional Research, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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Chen X, Lin Y, Qu Q, Ning B, Chen H, Liao B, Li X. Analyzing Association between Expression Quantitative Trait and CNV for Breast Cancer Based on Gene Interaction Network Clustering and Group Sparse Learning. Curr Bioinform 2022. [DOI: 10.2174/1574893617666220207095117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Aims:
The occurrence and development of tumor is accompanied by the change of pathogenic gene expression. Tumor cells avoid the damage of immune cells by regulating the expression of immune related genes.
Background:
Tracing the causes of gene expression variation is helpful to understand tumor evolution and metastasis.
Objective:
Current gene expression variation explanation methods are confronted with several main challenges: low explanation power, insufficient prediction accuracy, and lack of biological meaning.
Method:
In this study, we propose a novel method to analyze the mRNA expression variations of breast cancers risk genes. Firstly, we collected some high-confidence risk genes related to breast cancer and then designed a rank-based method to preprocess the breast cancers copy number variation (CNV) and mRNA data. Secondly, to elevate the biological meaning and narrow down the combinatorial space, we introduced a prior gene interaction network and applied a network clustering algorithm to generate high density subnetworks. Lastly, to describe the interlinked structure within and between subnetworks and target genes mRNA expression, we proposed a group sparse learning model to identify CNVs for pathogenic genes expression variations.
Result:
The performance of the proposed method is evaluated by both significantly improved predication accuracy and biological meaning of pathway enrichment analysis.
Conclusion:
The experimental results show that our method has practical significance
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Affiliation(s)
- Xia Chen
- College of Computer Science and Electronic Engineering, Hunan University, Changsha,
Hunan, China
- School of Basic Education, Changsha Aeronautical Vocational and Technical College,
Changsha, Hunan, China
| | - Yexiong Lin
- College of Computer Science and Electronic Engineering, Hunan University, Changsha,
Hunan, China
| | - Qiang Qu
- College of Computer Science and Electronic Engineering, Hunan University, Changsha,
Hunan, China
| | - Bin Ning
- College of Computer Science and Electronic Engineering, Hunan University, Changsha,
Hunan, China
| | - Haowen Chen
- College of Computer Science and Electronic Engineering, Hunan University, Changsha,
Hunan, China
| | - Bo Liao
- Ministry of Education, Hainan Normal University, Haikou, China
| | - Xiong Li
- School of Software, East China Jiaotong University, Nanchang, 330013, China
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Xu M, Chen Z, Lin B, Zhang S, Qu J. A seven-lncRNA signature for predicting prognosis in breast carcinoma. Transl Cancer Res 2022; 10:4033-4046. [PMID: 35116701 PMCID: PMC8797290 DOI: 10.21037/tcr-21-747] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022]
Abstract
Background Long non-coding RNAs (lncRNAs) play an important part in tumorigenesis and cancer metastasis and can serve as a potential biosignature for cancer prognosis. However, the use of lncRNA signatures to predict survival in breast carcinoma is yet unreported. Methods The lncRNA expression profiles and homologous clinical data of 913 breast carcinoma samples from the Cancer Genome Atlas (TCGA), were analyzed to obtain 2,547 differentially expressed lncRNAs. Univariate Cox proportional risk regression was applied to both the training and testing datasets to screen the common prognostic lncRNAs. Potential prognostic LncRNAs were screened by multivariate Cox proportional risk regression in the training data set of the selected LncRNAs. Results Seven lncRNAs (LINC02037, MAPT-AS1, RP1-37C10.3, RP11-344E13.4, RP11-454P21.1, RP11-616M22.1, SPACA6P-AS) were prominently associated with overall survival. Kaplan-Meier analysis and receiver operating characteristic (ROC) curves indicated that these indicators were sensitive and specific for survival prediction. The areas under the ROC curve of the seven-lncRNA signature in predicting 3- and 5-year survival rates were 0.771 and 0.780 respectively in the combined cohort. Furthermore, enrichment analysis revealed that these seven lncRNAs might participate multiple pathways related to tumorigenesis and prognosis. Conclusions The proposed seven-lncRNA signature could serve as a latent prognostic biomarker for survival prediction in patients with breast carcinoma.
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Affiliation(s)
- Min Xu
- Department of Operating Room, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Ziyan Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Bangyi Lin
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Sina Zhang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jinmiao Qu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Pairawan S, Akcakanat A, Kopetz S, Tapia C, Zheng X, Chen H, Ha MJ, Rizvi Y, Holla V, Wang J, Evans KW, Zhao M, Busaidy N, Fang B, Roth JA, Dumbrava EI, Meric-Bernstam F. Combined MEK/MDM2 inhibition demonstrates antitumor efficacy in TP53 wild-type thyroid and colorectal cancers with MAPK alterations. Sci Rep 2022; 12:1248. [PMID: 35075200 PMCID: PMC8786858 DOI: 10.1038/s41598-022-05193-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/14/2021] [Indexed: 11/08/2022] Open
Abstract
Most tumors with activating MAPK (mitogen-activated protein kinase) pathway alterations respond poorly to MEK inhibitors alone. Here, we evaluated combination therapy with MEK inhibitor selumetinib and MDM2 inhibitor KRT-232 in TP53 wild-type and MAPK altered colon and thyroid cancer models. In vitro, we showed synergy between selumetinib and KRT-232 on cell proliferation and colony formation assays. Immunoblotting confirmed p53 upregulation and MEK pathway inhibition. The combination was tested in vivo in seven patient-derived xenograft (PDX) models (five colorectal carcinoma and two papillary thyroid carcinoma models) with different KRAS, BRAF, and NRAS mutations. Combination therapy significantly prolonged event-free survival compared with monotherapy in six of seven models tested. Reverse-phase protein arrays and immunohistochemistry, respectively, demonstrated upregulation of the p53 pathway and in two models cleaved caspase 3 with combination therapy. In summary, combined inhibition of MEK and MDM2 upregulated p53 expression, inhibited MAPK signaling and demonstrated greater antitumor efficacy than single drug therapy in both in vitro and in vivo settings. These findings support further clinical testing of the MEK/MDM2 inhibitor combination in tumors of epithelial origin with MAPK pathway alterations.
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Affiliation(s)
- Seyed Pairawan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Argun Akcakanat
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Coya Tapia
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Epizyme Inc., Boston, USA
| | - Xiaofeng Zheng
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Huiqin Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Min Jin Ha
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yasmeen Rizvi
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Vijaykumar Holla
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Kurt W Evans
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ming Zhao
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Naifa Busaidy
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Bingliang Fang
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Jack A Roth
- Department of Thoracic and Cardiovascular Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Ecaterina Ileana Dumbrava
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Endocrine Neoplasia and Hormonal Disorders, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, 1400 Holcombe Blvd, FC8.3044, Houston, TX, 77030, USA.
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Ghafouri-Fard S, Sohrabi B, Hussen BM, Mehravaran E, Jamali E, Arsang-Jang S, Fathi M, Taheri M, Samsami M. Down-regulation of MEG3, PANDA and CASC2 as p53-related lncRNAs in breast cancer. Breast Dis 2022; 41:137-143. [PMID: 35034894 DOI: 10.3233/bd-210069] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
TP53 encodes a major tumor suppressor protein which blocks carcinogenesis process in a variety of tissues including breast tissue. Expression and function of this gene is regulated by a number of long non-coding RNAs (lncRNAs) among them are PANDA, MEG3 and CASC2. We measured expression of TP53 and these transcripts in a cohort of Iranian breast cancer patients. Expression levels of TP53, MEG3, CASC2 and PANDA were significantly lower in tumoral samples compared with non-tumoral samples (Posterior mean differences = -4.26, -1.66, -5.98 and -3.13, respectively; P values < 0.0001). Expression of CASC2 was higher in Her2 1+ cases compared with Her2 negative cases (Beta = 1.85, P value = 0.037). Expression levels of MEG3 and TP53 were lower in grade 2 samples compared with grade 1 (Beta = -1.86, P value = 0.006 and Beta = -2.24, P value = 0.003, respectively). There was no other significant association between expression of genes and clinical variables. CASC2 had the best performance among these genes with area under curve value of 0.78 and sensitivity and specificity values of 56.33% and 88.73%, respectively (P value < 0.0001). The current investigation supports the role of TP53-related lncRNAs in the pathogenesis of breast cancer.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Behnoush Sohrabi
- Department of Biology, Faculty of Sciences, Arak University, Arak, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Kurdistan Region, Iraq
| | - Elham Mehravaran
- Motamed Cancer Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Elena Jamali
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahram Arsang-Jang
- Cancer Gene Therapy Research Center, Zanjan University of Medical Science, Zanjan, Iran
| | - Mohadeseh Fathi
- Men's Health and Reproductive Health Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Majid Samsami
- Cancer Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Parmar HS, Nayak A, Kataria S, Tripathi V, Jaiswal P, Gavel PK, Jha HC, Bhagwat S, Dixit AK, Lukashevich V, Das AK, Sharma R. Restructuring the ONYX-015 adenovirus by using spike protein genes from SARS-CoV-2 and MERS-CoV: Possible implications in breast cancer treatment. Med Hypotheses 2022; 159:110750. [PMID: 35002022 PMCID: PMC8723760 DOI: 10.1016/j.mehy.2021.110750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/15/2021] [Accepted: 11/19/2021] [Indexed: 11/29/2022]
Affiliation(s)
| | - Aakruti Nayak
- School of Biotechnology, Devi Ahilya University, Indore 452001, M.P., India
| | - Shreya Kataria
- School of Biotechnology, Devi Ahilya University, Indore 452001, M.P., India
| | - Versha Tripathi
- School of Biotechnology, Devi Ahilya University, Indore 452001, M.P., India
| | - Pooja Jaiswal
- School of Biotechnology, Devi Ahilya University, Indore 452001, M.P., India
| | | | - Hem Chandra Jha
- Department of Bioscience and Bioengineering, IIT, Simrol, Indore, India
| | - Shivani Bhagwat
- Suraksha Diagnostics Pvt Ltd, Newtown, Rajarhat, Kolkata, West Bengal, India
| | - Amit Kumar Dixit
- Central Council for Research in Ayurvedic Sciences, Kolkata, West Bengal, India
| | - Vladimir Lukashevich
- Institute of Physiology of the National Academy of Sciences of Belarus, Minsk 220072, Belarus
| | - Apurba Kumar Das
- Department of Bioscience and Bioengineering, IIT, Simrol, Indore, India
| | - Rajesh Sharma
- School of Pharmacy, Devi Ahilya University, Indore 452001, M.P., India
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Galindo CM, Oliveira Ganzella FAD, Klassen G, Souza Ramos EAD, Acco A. Nuances of PFKFB3 signaling in breast cancer. Clin Breast Cancer 2022; 22:e604-e614. [DOI: 10.1016/j.clbc.2022.01.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/28/2021] [Accepted: 01/09/2022] [Indexed: 02/08/2023]
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Decidua Parietalis Mesenchymal Stem/Stromal Cells and Their Secretome Diminish the Oncogenic Properties of MDA231 Cells In Vitro. Cells 2021; 10:cells10123493. [PMID: 34944000 PMCID: PMC8700435 DOI: 10.3390/cells10123493] [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: 11/07/2021] [Revised: 11/28/2021] [Accepted: 11/30/2021] [Indexed: 12/27/2022] Open
Abstract
Mesenchymal stem cells (MSCs) have been shown to suppress tumor growth, inhibit angiogenesis, regulate cellular signaling, and induce apoptosis in cancer cells. We have earlier reported that placenta-derived decidua parietalis mesenchymal stem/stromal cells (DPMSCs) not only retained their functional characteristics in the cancer microenvironment but also exhibited increased expression of anti-apoptotic genes, demonstrating their anti-tumor properties in the tumor setting. In this study, we have further evaluated the effects of DPMSCs on the functional outcome of human breast cancer cell line MDA231. MDA231 cells were exposed to DPMSCs, and their biological functions, including adhesion, proliferation, migration, and invasion, were evaluated. In addition, genomic and proteomic modifications of the MDA231 cell line, in response to the DPMSCs, were also evaluated. MDA231 cells exhibited a significant reduction in proliferation, migration, and invasion potential after their treatment with DPMSCs. Furthermore, DPMSC treatment diminished the angiogenic potential of MDA231 cells. DPMSC treatment modulated the expression of various pro-apoptotic as well as oncogenes in MDA231 cells. The properties of DPMSCs to inhibit the invasive characteristics of MDA231 cells demonstrate that they may be a useful candidate in a stem-cell-based therapy against cancer.
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Yap KM, Sekar M, Wu YS, Gan SH, Rani NNIM, Seow LJ, Subramaniyan V, Fuloria NK, Fuloria S, Lum PT. Hesperidin and its aglycone hesperetin in breast cancer therapy: A review of recent developments and future prospects. Saudi J Biol Sci 2021; 28:6730-6747. [PMID: 34866972 PMCID: PMC8626310 DOI: 10.1016/j.sjbs.2021.07.046] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/11/2021] [Accepted: 07/14/2021] [Indexed: 01/05/2023] Open
Abstract
Breast cancer (BC) has high incidence and mortality rates, making it a major global health issue. BC treatment has been challenging due to the presence of drug resistance and the limited availability of therapeutic options for triple-negative and metastatic BC, thereby urging the exploration of more effective anti-cancer agents. Hesperidin and its aglycone hesperetin, two flavonoids from citrus species, have been extensively evaluated for their anti-cancer potentials. In this review, available literatures on the chemotherapeutic and chemosensitising activities of hesperidin and hesperetin in preclinical BC models are reported. The safety and bioavailability of hesperidin and hesperetin as well as the strategies to enhance their bioavailability are also discussed. Overall, hesperidin and hesperetin can inhibit cell proliferation, migration and BC stem cells as well as induce apoptosis and cell cycle arrest in vitro. They can also inhibit tumour growth, metastasis and neoplastic changes in tissue architecture in vivo. Moreover, the co-administration of hesperidin or hesperetin with doxorubicin, letrozole or tamoxifen can enhance the efficacies of these clinically available agents. These chemotherapeutic and chemosensitising activities of hesperidin and hesperetin have been linked to several mechanisms, including the modulation of signalling pathways, glucose uptake, enzymes, miRNA expression, oxidative status, cell cycle regulatory proteins, tumour suppressor p53, plasma and liver lipid profiles as well as DNA repair mechanisms. However, poor water solubility, extensive phase II metabolism and apical efflux have posed limitations to the bioavailability of hesperidin and hesperetin. Various strategies for bioavailability enhancement have been studied, including the utilisation of nano-based drug delivery systems and the co-administration of hesperetin with other flavonoids. In particular, nanoformulated hesperidin and hesperetin possess greater chemotherapeutic and chemosensitising activities than free compounds. Despite promising preclinical results, further safety and efficacy evaluation of hesperidin and hesperetin as well as their nanoformulations in clinical trials is required to ascertain their potentials to be developed as clinically useful agents for BC treatment.
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Affiliation(s)
- Kah Min Yap
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Health Sciences, Universiti Kuala Lumpur Royal College of Medicine Perak, Ipoh - 30450, Perak, Malaysia
| | - Mahendran Sekar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Health Sciences, Universiti Kuala Lumpur Royal College of Medicine Perak, Ipoh - 30450, Perak, Malaysia
| | - Yuan Seng Wu
- Faculty of Medicine, Bioscience and Nursing, MAHSA University, Selangor - 42610, Malaysia
| | - Siew Hua Gan
- School of Pharmacy, Monash University Malaysia, Bandar Sunway - 47500, Selangor Darul Ehsan, Malaysia
| | - Nur Najihah Izzati Mat Rani
- Faculty of Pharmacy and Health Sciences, Universiti Kuala Lumpur Royal College of Medicine Perak, Ipoh - 30450, Perak, Malaysia
| | - Lay Jing Seow
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Health Sciences, Universiti Kuala Lumpur Royal College of Medicine Perak, Ipoh - 30450, Perak, Malaysia
| | | | | | | | - Pei Teng Lum
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Health Sciences, Universiti Kuala Lumpur Royal College of Medicine Perak, Ipoh - 30450, Perak, Malaysia
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45
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Huang DP, Liao MM, Tong JJ, Yuan WQ, Peng DT, Lai JP, Zeng YH, Qiu YJ, Tong GD. Construction of a genome instability-derived lncRNA-based risk scoring system for the prognosis of hepatocellular carcinoma. Aging (Albany NY) 2021. [PMID: 34799469 DOI: 10.1863/aging.203698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
Abstract
Emerging evidence revealed the critical roles of long non-coding RNAs (lncRNAs) in maintaining genomic instability. However, genome instability-associated lncRNAs (GILncRNAs) and their performance in clinical prognostic significance in hepatocellular carcinoma (HCC) are rarely reported. Our study constructed a computational framework integrating somatic mutation information and lncRNA expression profiles of HCC genome and we identified 88 GILncRNAs of HCC. Function enrichment analysis revealed that GILncRNAs were involved in various metabolism processes and genome instability of cancer. A genome instability-derived lncRNA-based gene signature (GILncSig) was constructed using training set data. The performance of GILncSig for outcome prediction was validated in testing set and The Cancer Genome Atlas (TCGA) set. The multivariate cox regression analysis and stratification analysis demonstrated GILncSig could serve as an independent prognostic factor for the overall survival of HCC patients. The time-dependent Receiver Operating Characteristic (ROC) curve illustrated GILncSig outperformed two recently published lncRNA signatures for overall survival prediction. The combination of GILncSig and tumor protein p53 (TP53) mutation status exhibited better prognostic performance in survival evaluation compared to TP53 mutation status alone. AC145343.1 was further validated to be a risk factor for HCC in vitro among GILncSig. Overall, our study provided a novel approach for identification of genome instability-associated lncRNAs and established an independent risk score system for outcome prediction of HCC patients, which provided a new insight for exploring in-depth mechanism and potential therapy strategy.
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Affiliation(s)
- Dan-Ping Huang
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - Mian-Mian Liao
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China.,College of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510403, Guangdong, China
| | - Jing-Jing Tong
- The Affiliated Chencun Hospital of Shunde Hospital, Southern Medical University, Shunde 528300, Guangdong Province, China
| | - Wei-Qu Yuan
- Department of Acupuncture, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - De-Ti Peng
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - Jian-Ping Lai
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - Yi-Hao Zeng
- College of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510403, Guangdong, China
| | - Yi-Jun Qiu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510403, Guangdong Province, China
| | - Guang-Dong Tong
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
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46
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Huang DP, Liao MM, Tong JJ, Yuan WQ, Peng DT, Lai JP, Zeng YH, Qiu YJ, Tong GD. Construction of a genome instability-derived lncRNA-based risk scoring system for the prognosis of hepatocellular carcinoma. Aging (Albany NY) 2021; 13:24621-24639. [PMID: 34799469 PMCID: PMC8660619 DOI: 10.18632/aging.203698] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 10/25/2021] [Indexed: 12/25/2022]
Abstract
Emerging evidence revealed the critical roles of long non-coding RNAs (lncRNAs) in maintaining genomic instability. However, genome instability-associated lncRNAs (GILncRNAs) and their performance in clinical prognostic significance in hepatocellular carcinoma (HCC) are rarely reported. Our study constructed a computational framework integrating somatic mutation information and lncRNA expression profiles of HCC genome and we identified 88 GILncRNAs of HCC. Function enrichment analysis revealed that GILncRNAs were involved in various metabolism processes and genome instability of cancer. A genome instability-derived lncRNA-based gene signature (GILncSig) was constructed using training set data. The performance of GILncSig for outcome prediction was validated in testing set and The Cancer Genome Atlas (TCGA) set. The multivariate cox regression analysis and stratification analysis demonstrated GILncSig could serve as an independent prognostic factor for the overall survival of HCC patients. The time-dependent Receiver Operating Characteristic (ROC) curve illustrated GILncSig outperformed two recently published lncRNA signatures for overall survival prediction. The combination of GILncSig and tumor protein p53 (TP53) mutation status exhibited better prognostic performance in survival evaluation compared to TP53 mutation status alone. AC145343.1 was further validated to be a risk factor for HCC in vitro among GILncSig. Overall, our study provided a novel approach for identification of genome instability-associated lncRNAs and established an independent risk score system for outcome prediction of HCC patients, which provided a new insight for exploring in-depth mechanism and potential therapy strategy.
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Affiliation(s)
- Dan-Ping Huang
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - Mian-Mian Liao
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China.,College of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510403, Guangdong, China
| | - Jing-Jing Tong
- The Affiliated Chencun Hospital of Shunde Hospital, Southern Medical University, Shunde 528300, Guangdong Province, China
| | - Wei-Qu Yuan
- Department of Acupuncture, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - De-Ti Peng
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - Jian-Ping Lai
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
| | - Yi-Hao Zeng
- College of Basic Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510403, Guangdong, China
| | - Yi-Jun Qiu
- The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510403, Guangdong Province, China
| | - Guang-Dong Tong
- Department of Hepatology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen 518033, Guangdong Province, China
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47
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Rauf A, Abu-Izneid T, Thiruvengadam M, Imran M, Olatunde A, Shariati MA, Bawazeer S, Naz S, Shirooie S, Sanches-Silva A, Farooq U, Kazhybayeva G. Garlic (Allium sativum L.): Its Chemistry, Nutritional Composition, Toxicity and Anticancer Properties. Curr Top Med Chem 2021; 22:957-972. [PMID: 34749610 DOI: 10.2174/1568026621666211105094939] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 09/04/2021] [Accepted: 09/14/2021] [Indexed: 11/22/2022]
Abstract
The current review discuss the chemistry, nutritional composition, toxicity, and biological functions of garlic and its bioactive compounds against various types of cancers via different anticancer mechanisms. Several scientific documents were found in reliable literature and searched in databases viz Science Direct, PubMed, Web of Science, Scopus and Research Gate were carried out using keywords such as "garlic", "garlic bioactive compounds", "anticancer mechanisms of garlic", "nutritional composition of garlic", and others. Garlic contains several phytoconstituents with activities against cancer, and these compounds such as diallyl trisulfide (DATS), allicin, and diallyl disulfide (DADS), diallyl sulfide (DAS), and allyl mercaptan (AM). The influence of numerous garlic-derived products, phytochemicals, and nanoformulations on the liver, oral, prostate, breast, gastric, colorectal, skin, and pancreatic cancers has been studied. Based on our search, the bioactive molecules in garlic were found to inhibit the various phases of cancer. Moreover, the compounds in this plant also abrogate the peroxidation of lipids, activity of nitric oxide synthase, epidermal growth factor (EGF) receptor, nuclear factor-kappa B (NF-κB), protein kinase C, and regulate cell cycle and survival signaling cascades. Hence, garlic and its bioactive molecules exhibit the aforementioned mechanistic actions and thus, they could be used to inhibit the induction, development and progression of cancer. The review describes the nutritional Composition of garlic, its bioactive molecules, and nanoformulations against various types of cancers, as well as the potential for developing these agents as antitumor drugs.
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Affiliation(s)
- Abdur Rauf
- Department of Chemistry, University of Swabi, Swabi, Anbar 23430, KPK. Pakistan
| | - Tareq Abu-Izneid
- Pharmaceutical Sciences, College of Pharmacy, Al Ain University, Al Ain Campus. United Arab Emirates
| | - Muthu Thiruvengadam
- Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul 05029. South Korea
| | - Muhammad Imran
- University Institute of Diet & Nutritional Sciences, Faculty of Allied Health Sciences, The University of Lahore. Pakistan
| | - Ahmed Olatunde
- Department of Biochemistry, Abubakar Tafawa Balewa University, Bauchi 740272. Pakistan
| | - Mohammad Ali Shariati
- K.G. Razumovsky Moscow State University of Technologies and Management [the First Cossack University], Moscow. Russian Federation
| | - Saud Bawazeer
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Umm Al-Qura University, P.O. Box 42, Makkah. Saudi Arabia
| | - Saima Naz
- Department of Biotechnology, Bacha Khan University, Charsadda, KPK. Pakistan
| | - Samira Shirooie
- School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah. Iran
| | - Ana Sanches-Silva
- National Institute for Agricultural and Veterinary Research, 4485-655 Vila do Conde. Portugal
| | - Umar Farooq
- Department of Chemistry, COMSATS University Islamabad, Abbottabad-campus. Pakistan
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48
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Ho CH, Huang YJ, Lai YJ, Mukherjee R, Hsiao CK. The misuse of distributional assumptions in functional class scoring gene-set and pathway analysis. G3-GENES GENOMES GENETICS 2021; 12:6409857. [PMID: 34791175 PMCID: PMC8728032 DOI: 10.1093/g3journal/jkab365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/14/2021] [Indexed: 12/14/2022]
Abstract
Gene-set analysis (GSA) is a standard procedure for exploring potential biological functions of a group of genes. The development of its methodology has been an active research topic in recent decades. Many GSA methods, when newly proposed, rely on simulation studies to evaluate their performance with an implicit assumption that the multivariate expression values are normally distributed. This assumption is commonly adopted in GSAs, particularly those in the group of functional class scoring (FCS) methods. The validity of the normality assumption, however, has been disputed in several studies, yet no systematic analysis has been carried out to assess the effect of this distributional assumption. Our goal in this study is not to propose a new GSA method but to first examine if the multi-dimensional gene expression data in gene sets follow a multivariate normal (MVN) distribution. Six statistical methods in three categories of MVN tests were considered and applied to a total of 24 RNA data sets. These RNA values were collected from cancer patients as well as normal subjects, and the values were derived from microarray experiments, RNA sequencing, and single-cell RNA sequencing. Our first finding suggests that the MVN assumption is not always satisfied. This assumption does not hold true in many applications tested here. In the second part of this research, we evaluated the influence of non-normality on the statistical power of current FCS methods, both parametric and nonparametric ones. Specifically, the scenario of mixture distributions representing more than one population for the RNA values was considered. This second investigation demonstrates that the non-normality distribution of the RNA values causes a loss in the statistical power of these GSA tests, especially when subtypes exist. Among the FCS GSA tools examined here and among the scenarios studied in this research, the N-statistics outperform the others. Based on the results from these two investigations, we conclude that the assumption of MVN should be used with caution when evaluating new GSA tools, since this assumption cannot be guaranteed and violation may lead to spurious results, loss of power, and incorrect comparison between methods. If a newly proposed GSA tool is to be evaluated, we recommend the incorporation of a wide range of multivariate non-normal distributions or sampling from large databases if available.
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Affiliation(s)
- Chi-Hsuan Ho
- Division of Biostatistics and Data Science, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Yu-Jyun Huang
- Division of Biostatistics and Data Science, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 10055, Taiwan
| | - Ying-Ju Lai
- Division of Biostatistics and Data Science, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 10055, Taiwan
| | | | - Chuhsing Kate Hsiao
- Division of Biostatistics and Data Science, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei 10055, Taiwan.,Bioinformatics and Biostatistics Core, Center of Genomic Medicine, National Taiwan University, Taipei 10055, Taiwan
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49
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Lee HS, Lee IH, Kang K, Park SI, Kwon TW, Lee DY. A Network Pharmacology Analysis of the Systems-Perspective Anticancer Mechanisms of the Herbal Drug FDY2004 for Breast Cancer. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211049133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Breast cancer is a malignant tumor with high incidence, prevalence, and mortality rates in women. In recent years, herbal drugs have been assessed as anticancer therapy against breast cancer, owing to their promising therapeutic effects and reduced toxicity. However, their pharmacological mechanisms have not been fully explored at the systemic level. Here, we conducted a network pharmacology analysis of the systems-perspective molecular mechanisms of FDY2004, an anticancer herbal formula that consists of Moutan Radicis Cortex, Persicae Semen , and Rhei Radix et Rhizoma, against breast cancer. We determined that FDY2004 may contain 28 active compounds that exert pharmacological effects by targeting 113 breast cancer-related human genes/proteins. Based on the gene ontology terms, the FDY2004 targets were involved in modulating biological processes such as cell growth, cell proliferation, and apoptosis. Pathway enrichment analysis identified various breast cancer-associated pathways that may mediate the anticancer activity of FDY2004, including the PI3K-Akt, MAPK, TNF, HIF-1, focal adhesion, estrogen, ErbB, NF-kappa B, p53, and VEGF signaling pathways. Thus, our analysis offers novel insights into the anticancer properties of herbal drugs for breast cancer treatment from a systemic perspective.
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Affiliation(s)
- Ho-Sung Lee
- The Fore, 87 Ogeum-ro, Songpa-gu, Seoul 05542, Republic of Korea
- Forest Hospital, 129 Ogeum-ro, Songpa-gu, Seoul 05549, Republic of Korea
| | - In-Hee Lee
- The Fore, 87 Ogeum-ro, Songpa-gu, Seoul 05542, Republic of Korea
| | - Kyungrae Kang
- Forest Hospital, 129 Ogeum-ro, Songpa-gu, Seoul 05549, Republic of Korea
| | - Sang-In Park
- Forestheal Hospital, 173 Ogeum-ro, Songpa-gu, Seoul 05641, Republic of Korea
| | - Tae-Wook Kwon
- Forest Hospital, 129 Ogeum-ro, Songpa-gu, Seoul 05549, Republic of Korea
| | - Dae-Yeon Lee
- The Fore, 87 Ogeum-ro, Songpa-gu, Seoul 05542, Republic of Korea
- Forest Hospital, 129 Ogeum-ro, Songpa-gu, Seoul 05549, Republic of Korea
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50
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Lee HS, Lee IH, Kang K, Park SI, Jung M, Yang SG, Kwon TW, Lee DY. Network Pharmacology-Based Dissection of the Comprehensive Molecular Mechanisms of the Herbal Prescription FDY003 Against Estrogen Receptor-Positive Breast Cancer. Nat Prod Commun 2021. [DOI: 10.1177/1934578x211044377] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Estrogen receptor-positive breast cancer (ERPBC) is the commonest subtype of breast cancer, with a high prevalence, incidence, and mortality. Herbal drugs are increasingly being used to treat ERPBC, although their mechanisms of action are not fully understood. Therefore, in this study, we aimed to analyze the therapeutic properties of FDY003, a herbal anti-ERPBC prescription, using a network pharmacology approach. FDY003 decreased the viability of human ERPBC cells and sensitized them to tamoxifen, an endocrine drug that is widely used in the treatment of ERPBC. The network pharmacology analysis revealed 18 pharmacologically active components in FDY003 that may interact with and regulate 66 therapeutic targets. The enriched gene ontology terms for the FDY003 targets were associated with the modulation of cell survival and death, cell proliferation and growth arrest, and estrogen-associated cellular processes. Analysis of the pathway enrichment of the targets showed that FDY003 may target a variety of ERPBC-associated pathways, including the PIK3-Akt, focal adhesion, MAPK, and estrogen pathways. Overall, these data provide a comprehensive mechanistic insight into the anti-ERPBC activity of FDY003.
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Affiliation(s)
- Ho-Sung Lee
- The Fore, Seoul, Republic of Korea
- Forest Hospital, Seoul, Republic of Korea
| | | | | | | | - Minho Jung
- Forest Hospital, Seoul, Republic of Korea
| | | | | | - Dae-Yeon Lee
- The Fore, Seoul, Republic of Korea
- Forest Hospital, Seoul, Republic of Korea
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