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Su Y, Mei L, Jiang T, Wang Z, Ji Y. Novel role of lncRNAs regulatory network in papillary thyroid cancer. Biochem Biophys Rep 2024; 38:101674. [PMID: 38440062 PMCID: PMC10909982 DOI: 10.1016/j.bbrep.2024.101674] [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: 01/17/2024] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/06/2024] Open
Abstract
Papillary thyroid cancer (PTC) is the most common endocrine malignancy. The incidence of PTC has increased annually worldwide. Thus, PTC diagnosis and treatment attract more attention. Noncoding RNAs (lncRNAs) play crucial roles in PTC progression and act as prognostic biomarkers. Moreover, microRNAs (miRNAs) and epithelial-mesenchymal transition (EMT)-associated proteins have potential biomarkers for diagnosing and treating PTC. However, the correlation of lncRNAs with miRNAs and EMT-associated proteins needs further clarification. The present review highlights the recent advances of lncRNAs in PTC. We significantly summarized the two molecular regulatory mechanisms in PTC progress, including lncRNAs-miRNAs-protein signaling axes and lncRNAs-EMT pathways. This review will help our understanding of the association between lncRNAs and PTC and may assist us in evaluating the prognosis for PTC patients. Taken together, targeting the lncRNAs regulatory network has promising applications in diagnosing and treating PTC.
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Affiliation(s)
- Yuanhao Su
- Department of General Surgery, The Second Affiliated Hospital, Xi'an Jiaotong, University, Xi'an, 710004, China
| | - Lin Mei
- Scientific Research Center and Precision Medical Institute, The Second Affiliated, Hospital, Xi'an Jiaotong University, Xi'an, 710004, China
| | - Tiantian Jiang
- Department of General Surgery, The Second Affiliated Hospital, Xi'an Jiaotong, University, Xi'an, 710004, China
| | - Zhidong Wang
- Department of General Surgery, The Second Affiliated Hospital, Xi'an Jiaotong, University, Xi'an, 710004, China
| | - Yuanyuan Ji
- Scientific Research Center and Precision Medical Institute, The Second Affiliated, Hospital, Xi'an Jiaotong University, Xi'an, 710004, China
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2
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Lao C, Zheng P, Chen H, Liu Q, An F, Li Z. DeepAEG: a model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies. BMC Bioinformatics 2024; 25:105. [PMID: 38461284 PMCID: PMC10925015 DOI: 10.1186/s12859-024-05723-8] [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: 12/25/2023] [Accepted: 02/27/2024] [Indexed: 03/11/2024] Open
Abstract
MOTIVATION The prediction of cancer drug response is a challenging subject in modern personalized cancer therapy due to the uncertainty of drug efficacy and the heterogeneity of patients. It has been shown that the characteristics of the drug itself and the genomic characteristics of the patient can greatly influence the results of cancer drug response. Therefore, accurate, efficient, and comprehensive methods for drug feature extraction and genomics integration are crucial to improve the prediction accuracy. RESULTS Accurate prediction of cancer drug response is vital for guiding the design of anticancer drugs. In this study, we propose an end-to-end deep learning model named DeepAEG which is based on a complete-graph update mode to predict IC50. Specifically, we integrate an edge update mechanism on the basis of a hybrid graph convolutional network to comprehensively learn the potential high-dimensional representation of topological structures in drugs, including atomic characteristics and chemical bond information. Additionally, we present a novel approach for enhancing simplified molecular input line entry specification data by employing sequence recombination to eliminate the defect of single sequence representation of drug molecules. Our extensive experiments show that DeepAEG outperforms other existing methods across multiple evaluation parameters in multiple test sets. Furthermore, we identify several potential anticancer agents, including bortezomib, which has proven to be an effective clinical treatment option. Our results highlight the potential value of DeepAEG in guiding the design of specific cancer treatment regimens.
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Affiliation(s)
- Chuanqi Lao
- Research Center for Graph Computing, Zhejiang Lab, Yuhang, Hangzhou, 311121, Zhejiang, China
| | - Pengfei Zheng
- Research Center for Graph Computing, Zhejiang Lab, Yuhang, Hangzhou, 311121, Zhejiang, China
| | - Hongyang Chen
- Research Center for Graph Computing, Zhejiang Lab, Yuhang, Hangzhou, 311121, Zhejiang, China.
| | - Qiao Liu
- Department of Statistics, Stanford University, Stanford, Palo Alto, CA, 94305, USA
| | - Feng An
- Research Center for Graph Computing, Zhejiang Lab, Yuhang, Hangzhou, 311121, Zhejiang, China
| | - Zhao Li
- Research Center for Graph Computing, Zhejiang Lab, Yuhang, Hangzhou, 311121, Zhejiang, China
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Nosalova N, Huniadi M, Horňáková Ľ, Valenčáková A, Horňák S, Nagoos K, Vozar J, Cizkova D. Canine Mammary Tumors: Classification, Biomarkers, Traditional and Personalized Therapies. Int J Mol Sci 2024; 25:2891. [PMID: 38474142 DOI: 10.3390/ijms25052891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
In recent years, many studies have focused their attention on the dog as a proper animal model for human cancer. In dogs, mammary tumors develop spontaneously, involving a complex interplay between tumor cells and the immune system and revealing several molecular and clinical similarities to human breast cancer. In this review, we summarized the major features of canine mammary tumor, risk factors, and the most important biomarkers used for diagnosis and treatment. Traditional therapy of mammary tumors in dogs includes surgery, which is the first choice, followed by chemotherapy, radiotherapy, or hormonal therapy. However, these therapeutic strategies may not always be sufficient on their own; advancements in understanding cancer mechanisms and the development of innovative treatments offer hope for improved outcomes for oncologic patients. There is still a growing interest in the use of personalized medicine, which should play an irreplaceable role in the research not only in human cancer therapy, but also in veterinary oncology. Moreover, immunotherapy may represent a novel and promising therapeutic option in canine mammary cancers. The study of novel therapeutic approaches is essential for future research in both human and veterinary oncology.
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Affiliation(s)
- Natalia Nosalova
- Small Animal Clinic, University of Veterinary Medicine and Pharmacy, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Mykhailo Huniadi
- Small Animal Clinic, University of Veterinary Medicine and Pharmacy, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Ľubica Horňáková
- Small Animal Clinic, University of Veterinary Medicine and Pharmacy, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Alexandra Valenčáková
- Small Animal Clinic, University of Veterinary Medicine and Pharmacy, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Slavomir Horňák
- Small Animal Clinic, University of Veterinary Medicine and Pharmacy, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Kamil Nagoos
- Small Animal Clinic, University of Veterinary Medicine and Pharmacy, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Juraj Vozar
- Small Animal Clinic, University of Veterinary Medicine and Pharmacy, Komenskeho 73, 041 81 Kosice, Slovakia
| | - Dasa Cizkova
- Small Animal Clinic, University of Veterinary Medicine and Pharmacy, Komenskeho 73, 041 81 Kosice, Slovakia
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Ahn HM, Park I, Kim CG, Ko YK, Gim JA. Factors related to tumor response rate from TCGA three omics data-variants, expression, methylation. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART C, TOXICOLOGY AND CARCINOGENESIS 2024:1-16. [PMID: 38409772 DOI: 10.1080/26896583.2024.2319010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The Cancer Genome Atlas (TCGA) and its patient-derived multi-omics datasets have been the backbone of cancer research, and with novel approaches, it continues to shed new insight into the disease. In this study, we delved into a method of multi-omics integration of patient datasets and the association of biological pathways related to the disease. First, across thirty-three types of cancer present in TCGA, we merged genomic mutations and drug response datasets and filtered for the viable variant-drug response combinations available in TCGA, containing more than three samples for each drug response label with RNA sequencing (RNA-seq) and genomic methylation data available for each patient. We identified two distinct combinations in TCGA, one being pancreatic adenocarcinoma patients with/without rs121913529 variant in KRAS gene treated with gemcitabine, and the other low-grade glioma with/without rs121913500 variant in IDH1 gene administered with temozolomide. In these two groups, different patterns of gene expression were observed in the pathways often associated with cancer progression, such as mTOR and PDGF between the patients with complete response and progressive disease. Our result will provide yet another example of the relevance of these biological pathways in cancer drug response and a way for multi-omics integration in cancer datasets.
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Affiliation(s)
- Hyung-Min Ahn
- Center for Lung Cancer, National Cancer Center Hospital, Goyang, South Korea
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
| | - Insu Park
- BK21 Graduate Program, Department of Biomedical Sciences, Korea University College of Medicine, Seoul, South Korea
- Department of Laboratory Medicine, Korea University Guro Hospital, Seoul, South Korea
| | - Chang Geun Kim
- Center for Lung Cancer, National Cancer Center Hospital, Goyang, South Korea
- Department of Thoracic and Cardiovascular Surgery, Korea University Guro Hospital, Seoul, South Korea
| | - Young Kyung Ko
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul, South Korea
| | - Jeong-An Gim
- Department of Medical Science, Soonchunhyang University, Asan, South Korea
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Yayan J, Franke KJ, Berger M, Windisch W, Rasche K. Adhesion, metastasis, and inhibition of cancer cells: a comprehensive review. Mol Biol Rep 2024; 51:165. [PMID: 38252369 PMCID: PMC10803487 DOI: 10.1007/s11033-023-08920-5] [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: 08/25/2023] [Accepted: 10/23/2023] [Indexed: 01/23/2024]
Abstract
This comprehensive review delves into cancer's complexity, focusing on adhesion, metastasis, and inhibition. It explores the pivotal role of these factors in disease progression and therapeutic strategies. This review covers cancer cell migration, invasion, and colonization of distant organs, emphasizing the significance of cell adhesion and the intricate metastasis process. Inhibition approaches targeting adhesion molecules, such as integrins and cadherins, are discussed. Overall, this review contributes significantly to advancing cancer research and developing targeted therapies, holding promise for improving patient outcomes worldwide. Exploring different inhibition strategies revealed promising therapeutic targets to alleviate adhesion and metastasis of cancer cells. The effectiveness of integrin-blocking antibodies, small molecule inhibitors targeting Focal adhesion kinase (FAK) and the Transforming Growth Factor β (TGF-β) pathway, and combination therapies underscores their potential to disrupt focal adhesions and control epithelial-mesenchymal transition processes. The identification of as FAK, Src, β-catenin and SMAD4 offers valuable starting points for further research and the development of targeted therapies. The complex interrelationships between adhesion and metastatic signaling networks will be relevant to the development of new treatment approaches.
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Affiliation(s)
- Josef Yayan
- Department of Internal Medicine, Division of Pulmonary, Allergy, and Sleep Medicine, Witten/Herdecke University, HELIOS Clinic Wuppertal, Heusnerstr. 40, 42283, Wuppertal, Germany.
| | - Karl-Josef Franke
- Department of Internal Medicine, Pulmonary Division, Internal Intensive Care Medicine, Infectiology, and Sleep Medicine, Märkische Clinics Health Holding Ltd, Clinic Lüdenscheid, Witten/Herdecke University, Lüdenscheid, Germany
| | - Melanie Berger
- Department of Pneumology, Cologne Merheim Hospital, Witten/Herdecke University, Cologne, Germany
| | - Wolfram Windisch
- Department of Pneumology, Cologne Merheim Hospital, Witten/Herdecke University, Cologne, Germany
| | - Kurt Rasche
- Department of Internal Medicine, Division of Pulmonary, Allergy, and Sleep Medicine, Witten/Herdecke University, HELIOS Clinic Wuppertal, Heusnerstr. 40, 42283, Wuppertal, Germany
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Liu S, Tan DS, Graves N, Chacko AM. Economic Evaluations of Imaging Biomarker-Driven Companion Diagnostics for Cancer: A Systematic Review. APPLIED HEALTH ECONOMICS AND HEALTH POLICY 2023; 21:841-855. [PMID: 37747620 DOI: 10.1007/s40258-023-00833-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/07/2023] [Indexed: 09/26/2023]
Abstract
INTRODUCTION There is a boom in imaging biomarker-driven companion and complementary diagnostics (CDx) for cancer, which brings opportunity for personalized medicine. Whether adoption of these technologies is likely to be cost-effective is a relevant question, and studies on this topic are emerging. Despite the growing number of economic evaluations, no review of the methods used, quality of reporting, and potential risk of bias has been done. We report a systematic review to identify, summarize, and critique the cost-effectiveness evidence for the use of biomarker-driven and imaging-based CDx to inform cancer treatments. METHODS The Preferred Reporting Items of Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed. Systematic literature searches until 30 December 2022 were performed in PubMed, Web of Science, Medline, Embase, and Scopus for economic evaluations of imaging biomarker-based CDx for cancer. The inclusion and exclusion of studies were determined by pre-specified eligibility criteria informed by the 'Patient, Intervention, Comparison, Outcome' (PICO) framework. The Consolidated Health Economic Evaluation Reporting Standards (CHEERS) was used to assess the quality of reporting, and the Bias in Economic Evaluation (ECOBIAS) was used to examine the potential risk of bias of included studies. RESULTS A total of 12 papers were included, with eight model-based and four trial-based studies. Implementing biomarker-driven, imaging-based CDx was reported to be cost-effective, cost saving, or dominant (cost saving and more effective) in ten papers. Inconsistent methods were found in the studies, and the quality of reporting was lacking against the CHEERS reporting guideline. Several potential sources of 'risk of bias' were identified. These should be acknowledged and carefully considered by researchers planning future health economic evaluations. CONCLUSION Despite favorable results towards the implementation of imaging biomarker-based CDx for cancer, there is room for improvement regarding the quantity and quality of economic evaluations, and that is expected as the awareness of current study limitations increases and more clinical data become available in the future.
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Affiliation(s)
- Sibo Liu
- Health Services and Systems Research, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Daniel Sw Tan
- Cancer Therapeutics Research Laboratory, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168853, Singapore
| | - Nicholas Graves
- Health Services and Systems Research, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
| | - Ann-Marie Chacko
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168853, Singapore.
- Laboratory for Translational and Molecular Imaging, Programme in Cancer & Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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Dahmani S, Cerbito EF, Hamad A, Yusuff KB. Predictors of community pharmacists' readiness to manage the effective and safe use of oral anticancer medicines in a developing setting. J Oncol Pharm Pract 2023; 29:1580-1589. [PMID: 36426549 DOI: 10.1177/10781552221141696] [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] [Indexed: 10/28/2023]
Abstract
BACKGROUND There is a paucity of studies about the readiness of community pharmacists to manage the safe and effective use of oral anticancer medicines (OAMs) in developing settings. OBJECTIVES Using the readiness component (knowledge and willingness) of the situational theory of leadership, the study assessed community pharmacists' readiness to manage the safe and effective use of OAMs in Qatar, and also identified its significant predictors. METHODS A cross-sectional assessment of 252 community pharmacists was conducted with a pre-tested 48-item questionnaire. Readiness was assessed with a 5-point Likert-type scale and the maximum obtainable score was 70. The mean was used as the cut-off point to categorize willingness and knowledge as either high (≥ mean) or low (< mean). Independent t-test, one-way analysis of variance and multiple linear regression was used for data analyses. RESULTS The mean SD score for the readiness of community pharmacists was 39.3 ± 11.2 (min = 11, max = 70). Only a minority of the respondents expressed an excellent understanding of the chemotherapy cycles (19.6%; 45/230), and familiarity with targeted anticancer therapy (14.3%; 33/230), side effects (22.2%; 51/230), and dosing of OAMs (14.4%; 33/230). Employment status, number of OAMs prescriptions dispensed per month and adequacy of the contents related to OAMs in undergraduate training were the significant predictors of readiness (R2 = 0.558, (F (11, 209) = 3.559, p = 0.0001). CONCLUSIONS Community pharmacists' readiness appear inadequate especially regarding its dosing, side effects, handling, and disposal of OAMs. These inadequacies probably underline community pharmacists' low familiarity and comfortability with dispensing and educating patients on the effective and safe use of OAMs.
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Affiliation(s)
- Sara Dahmani
- Department of Clinical Pharmacy and Practice, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Emelith Florendo Cerbito
- Department of Clinical Pharmacy and Practice, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Anas Hamad
- Pharmacy Department, National Centre for Cancer Care and Research, Hamad Medical Corporation, Doha, Qatar
| | - Kazeem Babatunde Yusuff
- Department of Clinical Pharmacy and Practice, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
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Banda Sánchez C, Cubo Mateo N, Saldaña L, Valdivieso A, Earl J, González Gómez I, Rodríguez-Lorenzo LM. Selection and Optimization of a Bioink Based on PANC-1- Plasma/Alginate/Methylcellulose for Pancreatic Tumour Modelling. Polymers (Basel) 2023; 15:3196. [PMID: 37571089 PMCID: PMC10421301 DOI: 10.3390/polym15153196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/18/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
3D bioprinting involves using bioinks that combine biological and synthetic materials. The selection of the most appropriate cell-material combination for a specific application is complex, and there is a lack of consensus on the optimal conditions required. Plasma-loaded alginate and alginate/methylcellulose (Alg/MC) inks were chosen to study their viscoelastic behaviour, degree of recovery, gelation kinetics, and cell survival after printing. Selected inks showed a shear thinning behavior from shear rates as low as 0.2 s-1, and the ink composed of 3% w/v SA and 9% w/v MC was the only one showing a successful stacking and 96% recovery capacity. A 0.5 × 106 PANC-1 cell-laden bioink was extruded with an Inkredible 3D printer (Cellink) through a D = 410 μm tip conical nozzle into 6-well culture plates. Cylindrical constructs were printed and crosslinked with CaCl2. Bioinks suffered a 1.845 Pa maximum pressure at the tip that was not deleterious for cellular viability. Cell aggregates can be appreciated for the cut total length observed in confocal microscopy, indicating a good proliferation rate at different heights of the construct, and suggesting the viability of the selected bioink PANC-1/P-Alg3/MC9 for building up three-dimensional bioprinted pancreatic tumor constructs.
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Affiliation(s)
| | - Nieves Cubo Mateo
- Nebrija Research Group ARIES, Higher Polytechnic School, Antonio de Nebrija University, 28015 Madrid, Spain
- Institute for Physical and Information Technologies (ITEFI-CSIC), Sensors and Ultrasonic Systems, 28006 Madrid, Spain
| | - Laura Saldaña
- IdiPAZ, Hospital Universitario La Paz, 28046 Madrid, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine, CIBER-BBN, 28029 Madrid, Spain
| | - Alba Valdivieso
- Institute for Physical and Information Technologies (ITEFI-CSIC), Sensors and Ultrasonic Systems, 28006 Madrid, Spain
| | - Julie Earl
- Ramón y Cajal Health Research Institute (IRYCIS), Molecular Epidemiology and Predictive Tumour Markers, 28034 Madrid, Spain
- Biomedical Research Network in Cancer (CIBERONC), 28034 Madrid, Spain
| | - Itziar González Gómez
- Institute for Physical and Information Technologies (ITEFI-CSIC), Sensors and Ultrasonic Systems, 28006 Madrid, Spain
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Noor J, Chaudhry A, Noor R, Batool S. Advancements and Applications of Liquid Biopsies in Oncology: A Narrative Review. Cureus 2023; 15:e42731. [PMID: 37654932 PMCID: PMC10466971 DOI: 10.7759/cureus.42731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2023] [Indexed: 09/02/2023] Open
Abstract
According to the World Health Organization (WHO), nearly 10 million people died from cancer worldwide in 2020, making it the leading cause of mortality. Liquid biopsies, which provide non-invasive and real-time monitoring of tumor dynamics, have evolved into innovative diagnostic techniques in the field of oncology. Liquid biopsies offer important insights into tumor heterogeneity, treatment response, minimum residual disease identification, and personalized treatment of cancer through the analysis of circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), extracellular vesicles, and microRNAs. They offer several advantages over traditional tissue biopsies, such as being less invasive, more convenient, more representative of tumor heterogeneity and dynamics, and more informative for guiding personalized treatment decisions. Liquid biopsies are being utilized increasingly in clinical oncology, particularly for patients with metastatic disease who require ongoing monitoring and treatment modification. In this narrative review article, we review the latest developments of liquid biopsy technologies, their applications and limitations, and their potential to transform diagnosis, prognosis, and management of cancer patients.
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Affiliation(s)
- Jawad Noor
- Internal Medicine, St. Dominic Hospital, Jackson, USA
| | | | - Riwad Noor
- Medicine/Public Health, Nishtar Hospital, Multan, PAK
| | - Saima Batool
- Pathology, Nishtar Medical University, Multan, PAK
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Xu W, Mesa-Eguiagaray I, Kirkpatrick T, Devlin J, Brogan S, Turner P, Macdonald C, Thornton M, Zhang X, He Y, Li X, Timofeeva M, Farrington S, Din F, Dunlop M, Theodoratou E. Development and Validation of Risk Prediction Models for Colorectal Cancer in Patients with Symptoms. J Pers Med 2023; 13:1065. [PMID: 37511678 PMCID: PMC10381199 DOI: 10.3390/jpm13071065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
We aimed to develop and validate prediction models incorporating demographics, clinical features, and a weighted genetic risk score (wGRS) for individual prediction of colorectal cancer (CRC) risk in patients with gastroenterological symptoms. Prediction models were developed with internal validation [CRC Cases: n = 1686/Controls: n = 963]. Candidate predictors included age, sex, BMI, wGRS, family history, and symptoms (changes in bowel habits, rectal bleeding, weight loss, anaemia, abdominal pain). The baseline model included all the non-genetic predictors. Models A (baseline model + wGRS) and B (baseline model) were developed based on LASSO regression to select predictors. Models C (baseline model + wGRS) and D (baseline model) were built using all variables. Models' calibration and discrimination were evaluated through the Hosmer-Lemeshow test (calibration curves were plotted) and C-statistics (corrected based on 1000 bootstrapping). The models' prediction performance was: model A (corrected C-statistic = 0.765); model B (corrected C-statistic = 0.753); model C (corrected C-statistic = 0.764); and model D (corrected C-statistic = 0.752). Models A and C, that integrated wGRS with demographic and clinical predictors, had a statistically significant improved prediction performance. Our findings suggest that future application of genetic predictors holds significant promise, which could enhance CRC risk prediction. Therefore, further investigation through model external validation and clinical impact is merited.
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Affiliation(s)
- Wei Xu
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Ines Mesa-Eguiagaray
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Theresa Kirkpatrick
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Jennifer Devlin
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Medical Research Council, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Stephanie Brogan
- Clinical Research Team, Oncology Department, Forth Valley Royal Hospital, Stirling Road, Larbert FK5 4WR, UK
| | - Patricia Turner
- Clinical Research Team, Oncology Department, Forth Valley Royal Hospital, Stirling Road, Larbert FK5 4WR, UK
| | - Chloe Macdonald
- University Hospital Wishaw & University Hospital Monklands, NHS Lanarkshire, Airdrie ML6 0JS, UK
| | | | - Xiaomeng Zhang
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Yazhou He
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Xue Li
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Maria Timofeeva
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Medical Research Council, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- Danish Institute for Advanced Study, Research Unit of Epidemiology, Biostatistics and Biodemography, Institute of Public Health, University of Southern Denmark, 5230 Odense M, Denmark
| | - Susan Farrington
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Medical Research Council, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Farhat Din
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Medical Research Council, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Malcolm Dunlop
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit, Medical Research Council, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Evropi Theodoratou
- Centre for Global Health, Usher Institute, University of Edinburgh, Edinburgh EH8 9AG, UK
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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11
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Chetverina D, Vorobyeva NE, Gyorffy B, Shtil AA, Erokhin M. Analyses of Genes Critical to Tumor Survival Reveal Potential 'Supertargets': Focus on Transcription. Cancers (Basel) 2023; 15:cancers15113042. [PMID: 37297004 DOI: 10.3390/cancers15113042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/26/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023] Open
Abstract
The identification of mechanisms that underlie the biology of individual tumors is aimed at the development of personalized treatment strategies. Herein, we performed a comprehensive search of genes (termed Supertargets) vital for tumors of particular tissue origin. In so doing, we used the DepMap database portal that encompasses a broad panel of cell lines with individual genes knocked out by CRISPR/Cas9 technology. For each of the 27 tumor types, we revealed the top five genes whose deletion was lethal in the particular case, indicating both known and unknown Supertargets. Most importantly, the majority of Supertargets (41%) were represented by DNA-binding transcription factors. RNAseq data analysis demonstrated that a subset of Supertargets was deregulated in clinical tumor samples but not in the respective non-malignant tissues. These results point to transcriptional mechanisms as key regulators of cell survival in specific tumors. Targeted inactivation of these factors emerges as a straightforward approach to optimize therapeutic regimens.
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Affiliation(s)
- Darya Chetverina
- Group of Epigenetics, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Nadezhda E Vorobyeva
- Group of Dynamics of Transcriptional Complexes, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
| | - Balazs Gyorffy
- Departments of Bioinformatics and Pediatrics, Semmelweis University, H-1094 Budapest, Hungary
- Cancer Biomarker Research Group, Research Centre for Natural Sciences, Institute of Enzymology, H-1117 Budapest, Hungary
| | - Alexander A Shtil
- Blokhin National Medical Research Center of Oncology, 24 Kashirskoye Shosse, Moscow 115522, Russia
| | - Maksim Erokhin
- Group of Chromatin Biology, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilov Street, Moscow 119334, Russia
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12
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Maryam S, Krukiewicz K, Haq IU, Khan AA, Yahya G, Cavalu S. Interleukins (Cytokines) as Biomarkers in Colorectal Cancer: Progression, Detection, and Monitoring. J Clin Med 2023; 12:jcm12093127. [PMID: 37176567 PMCID: PMC10179696 DOI: 10.3390/jcm12093127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Cancer is the primary cause of death in economically developed countries and the second leading cause in developing countries. Colorectal cancer (CRC) is the third most common cause of cancer-related deaths worldwide. Risk factors for CRC include obesity, a diet low in fruits and vegetables, physical inactivity, and smoking. CRC has a poor prognosis, and there is a critical need for new diagnostic and prognostic biomarkers to reduce related deaths. Recently, studies have focused more on molecular testing to guide targeted treatments for CRC patients. The most crucial feature of activated immune cells is the production and release of growth factors and cytokines that modulate the inflammatory conditions in tumor tissues. The cytokine network is valuable for the prognosis and pathogenesis of colorectal cancer as they can aid in the cost-effective and non-invasive detection of cancer. A large number of interleukins (IL) released by the immune system at various stages of CRC can act as "biomarkers". They play diverse functions in colorectal cancer, and include IL-4, IL-6, IL-8, IL-11, IL-17A, IL-22, IL-23, IL-33, TNF, TGF-β, and vascular endothelial growth factor (VEGF), which are pro-tumorigenic genes. However, there are an inadequate number of studies in this area considering its correlation with cytokine profiles that are clinically useful in diagnosing cancer. A better understanding of cytokine levels to establish diagnostic pathways entails an understanding of cytokine interactions and the regulation of their various biochemical signaling pathways in healthy individuals. This review provides a comprehensive summary of some interleukins as immunological biomarkers of CRC.
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Affiliation(s)
- Sajida Maryam
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 44000, Pakistan
| | - Katarzyna Krukiewicz
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, M. Strzody 9, 44-100 Gliwice, Poland
- Centre for Organic and Nanohybrid Electronics, Silesian University of Technology, Konarskiego 22B, 44-100 Gliwice, Poland
| | - Ihtisham Ul Haq
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 44000, Pakistan
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, M. Strzody 9, 44-100 Gliwice, Poland
- Joint Doctoral School, Silesian University of Technology, Akademicka 2A, 44-100 Gliwice, Poland
| | - Awal Ayaz Khan
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 44000, Pakistan
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Al Sharqia, Egypt
- Department of Molecular Genetics, Faculty of Biology, Technical University of Kaiserslautern, Paul-Ehrlich Str. 24, 67663 Kaiserslautern, Germany
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 Decembrie 10, 410087 Oradea, Romania
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Finding miRNA-RNA Network Biomarkers for Predicting Metastasis and Prognosis in Cancer. Int J Mol Sci 2023; 24:ijms24055052. [PMID: 36902481 PMCID: PMC10003110 DOI: 10.3390/ijms24055052] [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: 01/16/2023] [Revised: 02/16/2023] [Accepted: 02/23/2023] [Indexed: 03/09/2023] Open
Abstract
Despite remarkable progress in cancer research and treatment over the past decades, cancer ranks as a leading cause of death worldwide. In particular, metastasis is the major cause of cancer deaths. After an extensive analysis of miRNAs and RNAs in tumor tissue samples, we derived miRNA-RNA pairs with substantially different correlations from those in normal tissue samples. Using the differential miRNA-RNA correlations, we constructed models for predicting metastasis. A comparison of our model to other models with the same data sets of solid cancer showed that our model is much better than the others in both lymph node metastasis and distant metastasis. The miRNA-RNA correlations were also used in finding prognostic network biomarkers in cancer patients. The results of our study showed that miRNA-RNA correlations and networks consisting of miRNA-RNA pairs were more powerful in predicting prognosis as well as metastasis. Our method and the biomarkers obtained using the method will be useful for predicting metastasis and prognosis, which in turn will help select treatment options for cancer patients and targets of anti-cancer drug discovery.
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14
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Hopkins CE. Emerging technologies in personalized medicine. Mol Aspects Med 2023; 91:101182. [PMID: 36804860 DOI: 10.1016/j.mam.2023.101182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
A variety of technologies are emerging to help clinicians provide patient-specific diagnosis and therapies. This special edition of the Molecular Aspects of Medicine is a collection of mini reviews covering a broad range of topics, from systems to model patient variants and discover therapies (Microphysiological systems with patient derived tissue and CRISPR-humanized animal models), to new modalities in diagnostics and therapeutics (Extracellular Vesicles, RNA therapeutics, microbiome and molecular dynamics).
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E3 Ubiquitin Ligase TRIP12 Controls Exit from Mitosis via Positive Regulation of MCL-1 in Response to Taxol. Cancers (Basel) 2023; 15:cancers15020505. [PMID: 36672454 PMCID: PMC9856375 DOI: 10.3390/cancers15020505] [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: 11/16/2022] [Revised: 12/23/2022] [Accepted: 12/31/2022] [Indexed: 01/18/2023] Open
Abstract
Chemotherapy resistance is a major hurdle in cancer treatment. Taxol-based chemotherapy is widely used in the treatment of cancers including breast, ovarian, and pancreatic cancer. Loss of function of the tumor suppressor F-box WD-40 domain containing 7 (FBW7) mutations leads to the accumulation of its substrate MCL-1 which is associated with Taxol resistance in human cancers. We recently showed that E3 ubiquitin ligase TRIP12 is a negative regulator of FBW7 protein. In this study, we find that Taxol-induced mitotic block in cancer cells is partly controlled by TRIP12 via its positive regulation of MCL-1 protein. Genetic inhibition of TRIP12 accelerates MCL-1 protein degradation in mitosis. Notably, introducing double-point mutations in lysines 404/412 of FBW7 to arginine which makes it resistant to proteasomal degradation, leads to the sharp reduction of MCL-1 protein levels and sensitizes cancer cells to Taxol-induced cell death. Finally, TRIP12 deletion leads to enhanced mitotic arrest and cell death in an FBW7 and MCL-1 dependent manner in multiple cell lines including colorectal and ovarian cancer but not in breast cancer. Thus, the TRIP12/FBW7/MCL-1 axis may provide a therapeutic target to overcome Taxol-associated chemotherapy resistance in cancer.
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16
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Saeed RF, Awan UA, Saeed S, Mumtaz S, Akhtar N, Aslam S. Targeted Therapy and Personalized Medicine. Cancer Treat Res 2023; 185:177-205. [PMID: 37306910 DOI: 10.1007/978-3-031-27156-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Targeted therapy and personalized medicine are novel emerging disciplines of cancer research intended for treatment and prevention. One of the most significant advancements in modern oncology is the shift from an organ-centric strategy to a personalized strategy guided by deep molecular analysis. This shift in view, which focuses on the tumour's precise molecular changes, has paved the way for individualized treatment. Researchers and clinicians are using targeted therapies to select the best treatment available based on the molecular characterization of malignant cancer. In the treatment of a cancer, personalized medicine entails the use of genetic, immunological, and proteomic profiling to provide therapeutic alternatives as well as prognostic information about cancer. In this book, targeted therapies and personalized medicine have been covered for specific malignancies, including latest FDA-approved targeted therapies and it also sheds light on effective anti-cancer regimens and drug resistance. This will help to enhance our ability to conduct individualized health planning, make early diagnoses, and choose optimal medications for each cancer patient with predictable side effects and outcomes in a quickly evolving era. Various applications and tools' capacity have been improved for early diagnosis of cancer and the growing number of clinical trials that choose specific molecular targets reflects this predicament. Nevertheless, there are several limitations that must need to be addressed. Hence, in this chapter, we will discuss recent advancements, challenges, and opportunities in personalized medicine for various cancers, with a specific emphasis on target therapies in diagnostics and therapeutics.
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Affiliation(s)
- Rida Fatima Saeed
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan.
| | - Uzma Azeem Awan
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | | | - Sara Mumtaz
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Nosheen Akhtar
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Shaista Aslam
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, Pakistan
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Hofmarcher T, Malmberg C, Lindgren P. A global analysis of the value of precision medicine in oncology - The case of non-small cell lung cancer. Front Med (Lausanne) 2023; 10:1119506. [PMID: 36891190 PMCID: PMC9986274 DOI: 10.3389/fmed.2023.1119506] [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: 12/08/2022] [Accepted: 01/30/2023] [Indexed: 02/22/2023] Open
Abstract
Objectives Biomarker testing is indispensable for the implementation of precision medicine (PM) in oncology. The aim of this study was to assess the value of biomarker testing from a holistic perspective based on the example of advanced non-small cell lung cancer (aNSCLC). Materials and methods A partitioned survival model was populated with data from pivotal clinical trials of first-line treatments in aNSCLC. Three testing scenarios were considered; "no biomarker testing" encompassing chemotherapy treatment, "sequential testing" for EGFR and ALK encompassing treatment with targeted- or chemotherapy, and "multigene testing" covering EGFR, ALK, ROS1, BRAF, NTRK, MET, RET and encompassing treatment with targeted- or immuno(chemo)therapy. Analyses of health outcomes and costs were run for nine countries (Australia, Brazil, China, Germany, Japan, Poland, South Africa, Turkey, United States). A 1-year and 5-year time horizon was applied. Information on test accuracy was combined with country-specific information on epidemiology and unit costs. Results Compared to the no-testing scenario, survival improved and treatment-related adverse events decreased with increased testing. Five-year survival increased from 2% to 5-7% and to 13-19% with sequential testing and multigene testing, respectively. The highest survival gains were observed in East Asia due to a higher local prevalence of targetable mutations. Overall costs increased with increased testing in all countries. Although costs for testing and medicines increased, costs for treatment of adverse events and end-of-life care decreased throughout all years. Non-health care costs (sick leave and disability pension payments) decreased during the first year but increased over a 5-year horizon. Conclusion The broad use of biomarker testing and PM in aNSCLC leads to more efficient treatment assignment and improves health outcomes for patients globally, in particular prolonged progression-free disease phase and overall survival. These health gains require investment in biomarker testing and medicines. While costs for testing and medicines would initially increase, cost decreases for other medical services and non-health care costs may partly offset the cost increases.
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Affiliation(s)
| | - Chiara Malmberg
- IHE-The Swedish Institute for Health Economics, Lund, Sweden
| | - Peter Lindgren
- IHE-The Swedish Institute for Health Economics, Lund, Sweden.,Karolinska Institutet, Solna, Sweden
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18
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Alotaibi F. Exosomal microRNAs in cancer: Potential biomarkers and immunotherapeutic targets for immune checkpoint molecules. Front Genet 2023; 14:1052731. [PMID: 36873941 PMCID: PMC9982116 DOI: 10.3389/fgene.2023.1052731] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 02/07/2023] [Indexed: 02/19/2023] Open
Abstract
Exosomes are small extracellular vesicles with a lipid bilayer structure secreted from different cell types which can be found in various body fluids including blood, pleural fluid, saliva and urine. They carry different biomolecules including proteins, metabolites, and amino acids such as microRNAs which are small non-coding RNAs that regulate gene expression and promote cell-to-cell communication. One main function of the exosomal miRNAs (exomiRs) is their role in cancer pathogenesis. Alternation in exomiRs expression could indicate disease progression and can regulate cancer growth and facilitate drug response/resistance. It can also influence the tumour microenvironment by controlling important signaling that regulating immune checkpoint molecules leading to activation of T cell anti-tumour immunity. Therefore, they can be used as potential novel cancer biomarkers and innovative immunotherapeutic agents. This review highlights the use of exomiRs as potential reliable biomarkers for cancer diagnosis, treatment response and metastasis. Finally, discuses their potential as immunotherapeutic agents to regulate immune checkpoint molecules and promote T cell anti-tumour immunity.
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Affiliation(s)
- Faizah Alotaibi
- College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences and King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
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19
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Tutty MA, Prina-Mello A. Three-Dimensional Spheroids for Cancer Research. Methods Mol Biol 2023; 2645:65-103. [PMID: 37202612 DOI: 10.1007/978-1-0716-3056-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In vitro cell culture is one of the most widely used tools used today for increasing our understanding of various things such as protein production, mechanisms of drug action, tissue engineering, and overall cellular biology. For the past decades, however, cancer researchers have relied heavily on conventional two-dimensional (2D) monolayer culture techniques to test a variety of aspects of cancer research ranging from the cytotoxic effects of antitumor drugs to the toxicity of diagnostic dyes and contact tracers. However, many promising cancer therapies have either weak or no efficacy in real-life conditions, therefore delaying or stopping altogether their translating to the clinic. This is, in part, due to the reductionist 2D cultures used to test these materials, which lack appropriate cell-cell contacts, have altered signaling, do not represent the natural tumor microenvironment, and have different drug responses, due to their reduced malignant phenotype when compared to real in vivo tumors. With the most recent advances, cancer research has moved into 3D biological investigation. Three-dimensional (3D) cultures of cancer cells not only recapitulate the in vivo environment better than their 2D counterparts, but they have, in recent years, emerged as a relatively low-cost and scientifically accurate methodology for studying cancer. In this chapter, we highlight the importance of 3D culture, specifically 3D spheroid culture, reviewing some key methodologies for forming 3D spheroids, discussing the experimental tools that can be used in conjunction with 3D spheroids and finally their applications in cancer research.
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Affiliation(s)
- Melissa Anne Tutty
- Laboratory for Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, Trinity College Dublin, Dublin, Ireland.
| | - Adriele Prina-Mello
- Laboratory for Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, Trinity College Dublin, Dublin, Ireland
- Nanomedicine and Molecular Imaging Group, Trinity Translational Medicine Institute, (TTMI), School of Medicine, Trinity College Dublin, Dublin, Ireland
- Trinity St. James's Cancer Institute, St. James's Hospital, Trinity College Dublin, Dublin, Ireland
- Advanced Materials and Bioengineering Research (AMBER) Centre, CRANN Institute, Trinity College Dublin, Dublin, Ireland
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20
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Lee W, Lee S, Han K. Constructing a Cancer Patient-Specific Network Based on Second-Order Partial Correlations of Gene Expression and DNA Methylation. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:266-276. [PMID: 35077366 DOI: 10.1109/tcbb.2022.3145796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Typically patient-specific gene networks are constructed with gene expression data only. Such networks cannot distinguish direct gene interactions from indirect interactions via others such as the effect of epigenetic events to gene activity. There is an increasing evidence of inter-individual variations not only in gene expression but also in epigenetic events such as DNA methylation. In this paper we propose a new method for constructing a cancer patient-specific gene correlation network using both gene expression and DNA methylation data. We derive a patient-specific network from differential second-order partial correlations of gene expression and DNA methylation between normal samples and the patient sample. The network represents direct interactions between genes by controlling the effect of DNA methylation. Using this method, we constructed 4,000 patient-specific networks for 10 types of cancer. The networks are highly effective in classifying different types of cancer and in deriving potential prognostic gene pairs. In particular, potential prognostic gene pairs derived from the networks were powerful in predicting the survival time of cancer patients. This approach will help identify patient-specific gene correlations and predict prognosis of cancer patients.
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21
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Tian F, Li F, Ren L, Wang Q, Jiang C, Zhang Y, Li M, Song X, Zhang S. Acoustic-Based Theranostic Probes Activated by Tumor Microenvironment for Accurate Tumor Diagnosis and Assisted Tumor Therapy. ACS Sens 2022; 7:3611-3633. [PMID: 36455009 DOI: 10.1021/acssensors.2c02129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Acoustic-based imaging techniques, including ultrasonography and photoacoustic imaging, are powerful noninvasive approaches for tumor imaging owing to sound transmission facilitation, deep tissue penetration, and high spatiotemporal resolution. Usually, imaging modes were classified into "always-on" mode and "activatable" mode. Conventional "always-on" acoustic-based probes often have difficulty distinguishing lesion regions of interest from surrounding healthy tissues due to poor target-to-background signal ratios. As compared, activatable probes have attracted attention with improved sensitivity, which can boost or amplify imaging signals only in response to specific biomolecular recognition or interactions. The tumor microenvironment (TME) exhibits abnormal physiological conditions that can be used to identify tumor sections from normal tissues. Various types of organic dyes and biomaterials can react with TME, leading to obvious changes in their optical properties. The TME also affects the self-assembly or aggregation state of nanoparticles, which can be used to design activatable imaging probes. Moreover, acoustic-based imaging probes and therapeutic agents can be coencapsulated into one nanocarrier to develop nanotheranostic probes, achieving tumor imaging and cooperative therapy. Satisfactorily, ultrasound waves not only accelerate the release of encapsulated therapeutic agents but also activate therapeutic agents to exert or enhance their therapeutic performance. Meanwhile, various photoacoustic probes can convert photon energy into heat under irradiation, achieving photoacoustic imaging and cooperative photothermal therapy. In this review, we focus on the recently developed TME-triggered ultrasound and photoacoustic theranostic probes for precise tumor imaging and targeted tumor therapy.
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Affiliation(s)
- Feng Tian
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276005, PR China
| | - Fengyan Li
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276005, PR China
| | - Linlin Ren
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276005, PR China
| | - Qi Wang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276005, PR China
| | - Chengfang Jiang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276005, PR China
| | - Yuqi Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276005, PR China
| | - Mengmeng Li
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276005, PR China
| | - Xinyue Song
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276005, PR China
| | - Shusheng Zhang
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Medicine, Linyi University, Linyi 276005, PR China
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22
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Espinoza Moya ME, Guertin JR, Dorval M, Lapointe J, Bouchard K, Nabi H, Laberge M. Examining interprofessional collaboration in oncogenetic service delivery models for hereditary cancers: a scoping review protocol. BMJ Open 2022; 12:e066802. [PMID: 36523215 PMCID: PMC9748975 DOI: 10.1136/bmjopen-2022-066802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION In a context of limited genetic specialists, collaborative models have been proposed to ensure timely access to high quality oncogenetic services for individuals with inherited cancer susceptibility. Yet, extensive variability in the terminology used and lack of a clear understanding of how interprofessional collaboration is operationalised and evaluated currently constrains the development of a robust evidence base on the value of different approaches used to optimise access to these services. To fill in this knowledge gap, this scoping review aims to systematically unpack the nature and extent of collaboration proposed by these interventions, and synthesise the evidence available on their implementation, effectiveness and economic impact. METHODS AND ANALYSIS Following the Joanna Briggs Institute guidelines for scoping reviews, a comprehensive literature search will be conducted to identify peer-reviewed and grey literature on collaborative models used for adult patients with, or at increased risk of, hereditary breast, ovarian, colorectal and prostate cancers. An initial search was developed for Medline, Embase, CINAHL (Cumulative Index to Nursing and Allied Health Literature), Cochrane and Web of Science on 13 June 2022 and will be complemented by searches in Google and relevant websites. Documents describing either the theory of change, planning, implementation and/or evaluation of these interventions will be considered for inclusion. Results will be summarised descriptively and used to compare relevant model characteristics and synthesise evidence available on their implementation, effectiveness and economic impact. This process is expected to guide the development of a definition and typology of collaborative models in oncogenetics that could help strengthen the knowledge base on these interventions. Moreover, because we will be mapping the existing evidence on collaborative models in oncogenetics, the proposed review will help us identify areas where additional research might be needed. ETHICS AND DISSEMINATION This research does not require ethics approval. Results from this review will be disseminated through peer-reviewed articles and conferences.
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Affiliation(s)
- Maria Eugenia Espinoza Moya
- Population Health and Optimal Health Practices Unit, Centre de Recherche du Centre hospitalier universitaire (CHU) de Québec-Université Laval, Quebec City, Quebec, Canada
- Département des opérations et systèmes de décision, Faculté des sciences de l'administration, Université Laval, Quebec City, Quebec, Canada
| | - Jason Robert Guertin
- Population Health and Optimal Health Practices Unit, Centre de Recherche du Centre hospitalier universitaire (CHU) de Québec-Université Laval, Quebec City, Quebec, Canada
- Department of Social and Preventive Medicine, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Michel Dorval
- Oncology Division, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, Quebec, Canada
- Faculty of Pharmacy, Université Laval, Quebec City, Quebec, Canada
- CISSS, Chaudière-Appalaches Research Center, Lévis, Québec, Canada
| | - Julie Lapointe
- Oncology Division, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Karine Bouchard
- Département de cancérologie, CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Hermann Nabi
- Department of Social and Preventive Medicine, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
- Oncology Division, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Maude Laberge
- Population Health and Optimal Health Practices Unit, Centre de Recherche du Centre hospitalier universitaire (CHU) de Québec-Université Laval, Quebec City, Quebec, Canada
- Département des opérations et systèmes de décision, Faculté des sciences de l'administration, Université Laval, Quebec City, Quebec, Canada
- Vitam, Centre de recherche en santé durable, Laval University, Quebec City, Quebec, Canada
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Zaszczyńska A, Niemczyk-Soczynska B, Sajkiewicz P. A Comprehensive Review of Electrospun Fibers, 3D-Printed Scaffolds, and Hydrogels for Cancer Therapies. Polymers (Basel) 2022; 14:polym14235278. [PMID: 36501672 PMCID: PMC9736375 DOI: 10.3390/polym14235278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 12/09/2022] Open
Abstract
Anticancer therapies and regenerative medicine are being developed to destroy tumor cells, as well as remodel, replace, and support injured organs and tissues. Nowadays, a suitable three-dimensional structure of the scaffold and the type of cells used are crucial for creating bio-inspired organs and tissues. The materials used in medicine are made of non-degradable and degradable biomaterials and can serve as drug carriers. Developing flexible and properly targeted drug carrier systems is crucial for tissue engineering, regenerative medicine, and novel cancer treatment strategies. This review is focused on presenting innovative biomaterials, i.e., electrospun nanofibers, 3D-printed scaffolds, and hydrogels as a novel approach for anticancer treatments which are still under development and awaiting thorough optimization.
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24
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Okubo Y, Yamamoto Y, Terao H, Suzuki T, Koizumi M, Yoshioka E, Washimi K, Sato S, Yokose T, Kishida T, Miyagi Y. Significance of non-standardized magnetic resonance imaging abnormalities and subsequent targeted prostate cancer biopsy for pathologists: A retrospective observational study. Pathol Res Pract 2022; 240:154188. [DOI: 10.1016/j.prp.2022.154188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 11/05/2022]
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25
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Ravi R, Mishra A, Anamika, Ahmad S. Fabrication of Superparamagnetic Bimetallic Magnesium Nanoferrite Using Green Polyol: Characterization and Anticancer Analysis in Vitro on Lung Cancer Cell Line A549. ACS APPLIED BIO MATERIALS 2022; 5:5365-5376. [PMID: 36326716 DOI: 10.1021/acsabm.2c00729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Magnetic bimetallic nanoparticles find many industrial and clinical applications in the field of water treatment, antibacterial and anticancer activities. Therefore, the current article reports green synthesis using oleo-polyol as a surface modifier and synthesis agent for bimetallic magnetic magnesium ferrite nanoparticles. The role of hydroxyl functionality of castor oil (a natural polyol) on the enhancement of structural, morphological, magnetic, and particle size properties has also been discussed. These properties were characterized using FTIR, XRD spectroscopy, SEM, AFM, and TEM microscopy, Brunauer-Emmett-Teller (BET), and vibrating sample magnetometer (VSM) techniques. The effect of calcination temperatures (600-900 °C) on particle size (23-40 nm to 500-600 nm), crystallite sizes (73.15-292.67 nm), and saturation magnetization (20.87, 23.07, 32.39, and 33.13 emu g-1) was analyzed. The influence of calcined temperatures on the anticancer activity of these nanoparticles has also been investigated in vitro using lung cancer cells (A549). Their biocompatibility, cytotoxicity, flow cytometry, and statistical analysis against lung cancer cells (A549) have been discussed. The green synthesis of magnesium nanoferrite particles using natural polyol and their application as anticancer agents against lung cancer cells (A549) have not been reported previously. They have exhibited far superior IC50 values and anticancer activity as compared to other reported metal oxides and magnesium oxide nanoparticles.
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Affiliation(s)
- Rangnath Ravi
- Department of Chemistry Shivaji College, University of Delhi, New Delhi 110027, India.,Natural Sciences & Department of Chemistry, Jamia Millia Islamia (Central University), New Delhi 110025, India
| | - Abhijeet Mishra
- Department of Biochemistry Shivaji College, University of Delhi, New Delhi 110027, India
| | - Anamika
- Center for Studies in Science Policy, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sharif Ahmad
- Natural Sciences & Department of Chemistry, Jamia Millia Islamia (Central University), New Delhi 110025, India
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Hassan S, Hassanain O, Kamal S, Shalaby L, Nagy M. Knowledge, attitudes and practices of Egyptian healthcare professionals toward therapeutic drug monitoring service as a principal component of personalized medicine. Per Med 2022; 19:509-521. [DOI: 10.2217/pme-2022-0031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: To assess pharmacists' and physicians' knowledge, attitudes and practices toward therapeutic drug monitoring (TDM) service at the Children's Cancer Hospital Egypt 57357. Materials & methods: This was a single-site cross-sectional study where all practicing pharmacists and physicians were eligible to participate. Results: A statistically significant difference in the knowledge scores between pharmacists and physicians (p = 0.022) was found. In general, attitudes toward TDM among pharmacists and physicians were positive. Regarding practices, pharmacists were more likely than physicians to agree or strongly agree that they have studied some scientific references on TDM (p = 0.034), but more physicians recommend the TDM service (p = 0.046). Conclusion: A multidisciplinary educational program in Egypt for TDM for both medicine and pharmacy staff will improve interprofessional collaboration in the clinical setting, leading to better personalized medication management.
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Affiliation(s)
- Sahar Hassan
- Department of Pharmaceutical Services, Children's Cancer Hospital Egypt, Cairo, 57357, Egypt
- Department of Clinical Pharmacy, Saarland University, Campus C5 3, Saarbrücken, 66123, Germany
| | - Omneya Hassanain
- Epidemiology and Biostatistics Unit, Department of Clinical Research, Children's Cancer Hospital Egypt, Cairo, 57357, Egypt
| | - Sherif Kamal
- Department of Pharmaceutical Services, Children's Cancer Hospital Egypt, Cairo, 57357, Egypt
| | - Lobna Shalaby
- Infectious Disease Unit, Children's Cancer Hospital Egypt, Cairo, 57357, Egypt
- Department of Pediatric Oncology, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Mohamed Nagy
- Department of Pharmaceutical Services, Children's Cancer Hospital Egypt, Cairo, 57357, Egypt
- Personalized Medication Management Unit, Children's Cancer Hospital Egypt, Cairo, 57357, Egypt
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Boppudi SM, Scheil-Bertram S, Faust E, Annamneedi A, Fisseler-Eckhoff A. Assessing and Evaluating the Scope and Constraints of Idylla Molecular Assays by Using Different Source Materials in Routine Diagnostic Settings. Int J Mol Sci 2022; 23:ijms232012515. [PMID: 36293374 PMCID: PMC9604085 DOI: 10.3390/ijms232012515] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
For cancer treatment, diagnostics concerning tumor type and determination of molecular markers in short TAT is critical. The fully automated, real-time PCR-based molecular diagnostic Idylla assays are well established in many laboratories for qualitative detection, short TAT and routine screening of clinically relevant oncogenic mutations. According to the manufacturer, all IVD assays are recommended for use only with FFPE tissue samples of 5–10 µM dissections with at least 10% tumor content. In this study, we tested the performance and accuracy of the IVD assays along with the gene fusion assay (RUO) with different tissue/source materials like isolated DNA/RNA, cryomaterial, etc. The study also included testing archival FFPE tissue sections dating back from 20 years and a performance check for different pan-cancer samples individually. All the assays tested with FFPE sections and gDNA/RNA input showed above 96% accuracy and sensitivity, individually with 100% specificity. The Idylla assays also performed exceptionally well on the archival FFPE tissues, and the use of assays for other solid tumors was also remarkable. The performance test and accuracy of Idylla assays showed high efficiency with certain limitations. For the use of Idylla assays, both qualitative and quantitative applicability of different tumor source materials could produce efficient results in different diagnostic settings within a short TAT.
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Affiliation(s)
- Sanga Mitra Boppudi
- Helios Dr. Horst Schmidt Kliniken Wiesbaden, Institute for Pathology and Cytology, 65199 Wiesbaden, Germany
- Gemeinschaftspraxis für Pathologie, 65199 Wiesbaden, Germany
- Correspondence: (S.M.B.); (A.F.-E.)
| | - Stefanie Scheil-Bertram
- Helios Dr. Horst Schmidt Kliniken Wiesbaden, Institute for Pathology and Cytology, 65199 Wiesbaden, Germany
| | - Elisabeth Faust
- Helios Dr. Horst Schmidt Kliniken Wiesbaden, Institute for Pathology and Cytology, 65199 Wiesbaden, Germany
| | - Anil Annamneedi
- Team Biology of GPCR Signaling Systems (BIOS), CNRS, IFCE, INRAE, Université de Tours, Physiologie de la Reproduction et des Comportements (PRC), 37380 Nouzilly, France
- LE STUDIUM Loire Valley Institute for Advanced Studies, 45000 Orléans, France
| | - Annette Fisseler-Eckhoff
- Helios Dr. Horst Schmidt Kliniken Wiesbaden, Institute for Pathology and Cytology, 65199 Wiesbaden, Germany
- Gemeinschaftspraxis für Pathologie, 65199 Wiesbaden, Germany
- Correspondence: (S.M.B.); (A.F.-E.)
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28
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Eskandarion MR, Tizmaghz Z, Andalib B, Parsa N, Emami SAH, Shahsiah R, Oghabian MA, Shirkoohi R. A case report of the sustained and rapid response of bevacizumab in a TP53-positive breast cancer and liver metastatic patient through personalized medicine. Front Oncol 2022; 12:940678. [PMID: 36119510 PMCID: PMC9479335 DOI: 10.3389/fonc.2022.940678] [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: 05/10/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022] Open
Abstract
HER2-positive metastatic breast cancer is much less frequent than other subgroups of breast cancer. Treatment options for this cancer are mostly limited to systemic chemotherapy, which leads to moderate improvements. Targeted therapy against malignant breast cancer requires the identification of reliable biomarkers for personalized medicine to obtain the maximum benefit of this therapy. Any mutations in the TP53 signaling pathway can be considered as a significant causative factor of breast cancer, for which the identification of target genes plays an important role in selecting the appropriate treatment. The use of personalized gene expression profiling could be valuable to find the direct target of the treatment in this case. The present study assessed the genetic profile of an HER2-positive metastatic breast cancer patient (with a liver metastasis) and figured out a complete and sustained response to bevacizumab. According to the results of next-generation sequencing (NGS) analysis, the patient’s genetic profile showed an increased expression of p4EBP1 and PTEN and the activation of the mTOR signaling pathway with a mutation in the TP53 gene. Based on the common treatment of similar profiling, we administrated bevacizumab/Taxol/Gemzar chemotherapy up to six courses. Accordingly, as the response to treatment was revealed by reducing the volume of the liver metastasis from 4 to 1.4 cm, metastasectomy was performed as a complementary treatment. Hence, personalized gene expression profiling not only is useful for targeted therapy but also could be recommended to avoid prescription of non-responsive drugs.
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Affiliation(s)
- Mohammad Reza Eskandarion
- Cancer Research Center, Cancer Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
- BESTforPM (Biomarker Evaluation and Supervision Team for Personalized Medicine), Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Tizmaghz
- BESTforPM (Biomarker Evaluation and Supervision Team for Personalized Medicine), Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
- Department of Radiation Oncology, Cancer Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahram Andalib
- BESTforPM (Biomarker Evaluation and Supervision Team for Personalized Medicine), Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
- Radiation Oncology Central Clinic of Karaj (ROCK), Karaj, Iran
- *Correspondence: Reza Shirkoohi, ; Bahram Andalib,
| | - Nasser Parsa
- BESTforPM (Biomarker Evaluation and Supervision Team for Personalized Medicine), Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
- Iranian Cancer Association, Tehran, Iran
| | - Seyed Amir Hossein Emami
- Cancer Research Center, Cancer Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
- BESTforPM (Biomarker Evaluation and Supervision Team for Personalized Medicine), Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
- Department of Hematology and Medical Oncology, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Shahsiah
- BESTforPM (Biomarker Evaluation and Supervision Team for Personalized Medicine), Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
- Department of Anatomical and Clinical Pathology, Cancer Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Ali Oghabian
- BESTforPM (Biomarker Evaluation and Supervision Team for Personalized Medicine), Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
- Medical Physics Department, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Shirkoohi
- Cancer Research Center, Cancer Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
- BESTforPM (Biomarker Evaluation and Supervision Team for Personalized Medicine), Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
- *Correspondence: Reza Shirkoohi, ; Bahram Andalib,
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29
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Acute myelogenous leukemia – current recommendations and approaches in molecular-genetic assessment. ROMANIAN JOURNAL OF INTERNAL MEDICINE 2022; 60:103-114. [DOI: 10.2478/rjim-2022-0004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Indexed: 11/20/2022] Open
Abstract
Abstract
Acute myelogenous leukemia is a multi-step hematological malignancy, affecting function, growth, proliferation and cell cycle of myeloid precursors. Overall assessment of patients with the disease requires among everything else, a comprehensive investigation of the genetic basis through various methods such as cytogenetic and molecular-genetic ones. This clarification provides diagnostic refinement and carries prognostic and predictive value in respect of essential therapeutic choices.
With this review of the literature, we focus on summarizing the latest recommendations and preferred genetic methods, as well as on emphasizing on their general benefits and limitations. Since none of these methods is actually totipotent, we also aim to shed light over the often-difficult choice of appropriate genetic analyses.
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30
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Sudhakar M, Rengaswamy R, Raman K. Multi-Omic Data Improve Prediction of Personalized Tumor Suppressors and Oncogenes. Front Genet 2022; 13:854190. [PMID: 35620468 PMCID: PMC9127508 DOI: 10.3389/fgene.2022.854190] [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: 01/13/2022] [Accepted: 04/04/2022] [Indexed: 12/12/2022] Open
Abstract
The progression of tumorigenesis starts with a few mutational and structural driver events in the cell. Various cohort-based computational tools exist to identify driver genes but require multiple samples to identify less frequently mutated driver genes. Many studies use different methods to identify driver mutations/genes from mutations that have no impact on tumor progression; however, a small fraction of patients show no mutational events in any known driver genes. Current unsupervised methods map somatic and expression data onto a network to identify personalized driver genes based on changes in expression. Our method is the first machine learning model to classify genes as tumor suppressor gene (TSG), oncogene (OG), or neutral, thus assigning the functional impact of the gene in the patient. In this study, we develop a multi-omic approach, PIVOT (Personalized Identification of driVer OGs and TSGs), to train on experimentally or computationally validated mutational and structural driver events. Given the lack of any gold standards for the identification of personalized driver genes, we label the data using four strategies and, based on classification metrics, show gene-based labeling strategies perform best. We build different models using SNV, RNA, and multi-omic features to be used based on the data available. Our models trained on multi-omic data improved predictions compared with mutation and expression data, achieving an accuracy ≥0.99 for BRCA, LUAD, and COAD datasets. We show network and expression-based features contribute the most to PIVOT. Our predictions on BRCA, COAD, and LUAD cancer types reveal commonly altered genes such as TP53 and PIK3CA, which are predicted drivers for multiple cancer types. Along with known driver genes, our models also identify new driver genes such as PRKCA, SOX9, and PSMD4. Our multi-omic model labels both CNV and mutations with a more considerable contribution by CNV alterations. While predicting labels for genes mutated in multiple samples, we also label rare driver events occurring in as few as one sample. We also identify genes with dual roles within the same cancer type. Overall, PIVOT labels personalized driver genes as TSGs and OGs and also identified rare driver genes.
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Affiliation(s)
- Malvika Sudhakar
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, India.,Robert Bosch Center for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India.,Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras, Chennai, India
| | - Raghunathan Rengaswamy
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, India.,Robert Bosch Center for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India.,Department of Chemical Engineering, IIT Madras, Chennai, India
| | - Karthik Raman
- Centre for Integrative Biology and Systems mEdicine (IBSE), Indian Institute of Technology (IIT) Madras, Chennai, India.,Robert Bosch Center for Data Science and Artificial Intelligence (RBCDSAI), IIT Madras, Chennai, India.,Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, IIT Madras, Chennai, India
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31
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Hartung M, Anastasi E, Mamdouh ZM, Nogales C, Schmidt HHHW, Baumbach J, Zolotareva O, List M. Cancer driver drug interaction explorer. Nucleic Acids Res 2022; 50:W138-W144. [PMID: 35580047 PMCID: PMC9252786 DOI: 10.1093/nar/gkac384] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/06/2022] [Accepted: 04/29/2022] [Indexed: 12/16/2022] Open
Abstract
Cancer is a heterogeneous disease characterized by unregulated cell growth and promoted by mutations in cancer driver genes some of which encode suitable drug targets. Since the distinct set of cancer driver genes can vary between and within cancer types, evidence-based selection of drugs is crucial for targeted therapy following the precision medicine paradigm. However, many putative cancer driver genes can not be targeted directly, suggesting an indirect approach that considers alternative functionally related targets in the gene interaction network. Once potential drug targets have been identified, it is essential to consider all available drugs. Since tools that offer support for systematic discovery of drug repurposing candidates in oncology are lacking, we developed CADDIE, a web application integrating six human gene-gene and four drug-gene interaction databases, information regarding cancer driver genes, cancer-type specific mutation frequencies, gene expression information, genetically related diseases, and anticancer drugs. CADDIE offers access to various network algorithms for identifying drug targets and drug repurposing candidates. It guides users from the selection of seed genes to the identification of therapeutic targets or drug candidates, making network medicine algorithms accessible for clinical research. CADDIE is available at https://exbio.wzw.tum.de/caddie/ and programmatically via a python package at https://pypi.org/project/caddiepy/.
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Affiliation(s)
- Michael Hartung
- Institute for Computational Systems Biology, University of Hamburg, 22607 Hamburg, Germany
| | - Elisa Anastasi
- School of Computing, Newcastle University, 2308 Newcastle upon Tyne, UK
| | - Zeinab M Mamdouh
- Department of Pharmacology and Personalised Medicine, Maastricht University, 6229 Maastricht, Netherlands.,Department of Pharmacology and Toxicology, Faculty of Pharmacy, Zagazig University, 44519 Zagazig, Egypt
| | - Cristian Nogales
- Department of Pharmacology and Personalised Medicine, Maastricht University, 6229 Maastricht, Netherlands
| | - Harald H H W Schmidt
- Department of Pharmacology and Personalised Medicine, Maastricht University, 6229 Maastricht, Netherlands
| | - Jan Baumbach
- Institute for Computational Systems Biology, University of Hamburg, 22607 Hamburg, Germany.,Computational Biomedicine Lab, Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense, Denmark
| | - Olga Zolotareva
- Institute for Computational Systems Biology, University of Hamburg, 22607 Hamburg, Germany.,Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Markus List
- Chair of Experimental Bioinformatics, TUM School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
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32
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p53 mutants G245S and R337H associated with the Li-Fraumeni syndrome regulate distinct metabolic pathways. Biochimie 2022; 198:141-154. [DOI: 10.1016/j.biochi.2022.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 12/13/2022]
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Immune-Proteome Profiling in Classical Hodgkin Lymphoma Tumor Diagnostic Tissue. Cancers (Basel) 2021; 14:cancers14010009. [PMID: 35008176 PMCID: PMC8750205 DOI: 10.3390/cancers14010009] [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: 11/14/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
In classical Hodgkin Lymphoma (cHL), immunoediting via protein signaling is key to evading tumor surveillance. We aimed to identify immune-related proteins that distinguish diagnostic cHL tissues (=diagnostic tumor lysates, n = 27) from control tissues (reactive lymph node lysates, n = 30). Further, we correlated our findings with the proteome plasma profile between cHL patients (n = 26) and healthy controls (n = 27). We used the proximity extension assay (PEA) with the OlinkTM multiplex Immuno-Oncology panel, consisting of 92 proteins. Univariate, multivariate-adjusted analysis and Benjamini–Hochberg’s false discovery testing (=Padj) were performed to detect significant discrepancies. Proteins distinguishing cHL cases from controls were more numerous in plasma (30 proteins) than tissue (17 proteins), all Padj < 0.05. Eight of the identified proteins in cHL tissue (PD-L1, IL-6, CCL17, CCL3, IL-13, MMP12, TNFRS4, and LAG3) were elevated in both cHL tissues and cHL plasma compared with control samples. Six proteins distinguishing cHL tissues from controls tissues were significantly correlated to PD-L1 expression in cHL tissue (IL-6, MCP-2, CCL3, CCL4, GZMB, and IFN-gamma, all p ≤0.05). In conclusion, this study introduces a distinguishing proteomic profile in cHL tissue and potential immune-related markers of pathophysiological relevance.
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34
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Quo vadis artificial intelligence and personalized medicine? FUTURE DRUG DISCOVERY 2021. [DOI: 10.4155/fdd-2021-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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35
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Soofiyani SR, Hosseini K, Soleimanian A, Abkhooei L, Hoseini AM, Tarhriz V, Ghasemnejad T. An Overview on the Role of miR-451 in Lung Cancer: Diagnosis, Therapy, and Prognosis. Microrna 2021; 10:181-190. [PMID: 34514995 DOI: 10.2174/2211536610666210910130828] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/15/2021] [Accepted: 08/03/2021] [Indexed: 11/22/2022]
Abstract
MicroRNAs (miRNAs) are highly conserved non-coding RNAs involved in many physiological processes such as cell proliferation, inhibition, development of apoptosis, differentiation, suppresses tumorigenicity, and regulating cell growth. The description of the alterations of miRNA expression patterns in cancers will be helpful to recognize biomarkers for early detection and possible therapeutic intervention in the treatment of cancers. Recent studies have shown that miR-451 is broadly dysregulated in lung cancer and is a crucial agent in lung tumor progression. This review summarizes recent advances of the potential role of miR-451 in lung cancer diagnosis, prognosis, and treatment and provides an insight into the potential use of miR-451 for the development of advanced therapeutic methods in lung cancer.
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Affiliation(s)
- Saiedeh Razi Soofiyani
- Clinical Research Development Unit of Sina Educational, Research and Treatment Center, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Kamram Hosseini
- Student research committee, Shiraz University of Medical Sciences, Shiraz. Iran
| | - Alireza Soleimanian
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz. Iran
| | - Liela Abkhooei
- Department of Medical Biotechnology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad. Iran
| | - Akbar Mohammad Hoseini
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine and Tabriz Blood Transfusion Center, Tabriz. Iran
| | - Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz. Iran
| | - Tohid Ghasemnejad
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz. Iran
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36
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Kabwe M, Dashper S, Bachrach G, Tucci J. Bacteriophage manipulation of the microbiome associated with tumour microenvironments-can this improve cancer therapeutic response? FEMS Microbiol Rev 2021; 45:6188389. [PMID: 33765142 DOI: 10.1093/femsre/fuab017] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/21/2021] [Indexed: 12/11/2022] Open
Abstract
Some cancer treatment failures have been attributed to the tumour microbiota, with implications that microbiota manipulation may improve treatment efficacy. While antibiotics have been used to control bacterial growth, their dysbiotic effects on the microbiome, failure to penetrate biofilms and decreased efficacy due to increasing antimicrobial resistance by bacteria, suggest alternatives are needed. Bacteriophages may provide a precise means for targeting oncobacteria whose relative abundance is increased in tumour tissue microbiomes. Fusobacterium, Streptococcus, Peptostreptococcus, Prevotella, Parvimonas, and Treponema species are prevalent in tumour tissue microbiomes of some cancers. They may promote cancer growth by dampening immunity, stimulating release of proinflammatory cytokines, and directly interacting with cancer cells to stimulate proliferation. Lytic bacteriophages against some of these oncobacteria have been isolated and characterised. The search continues for others. The possibility exists for their testing as adjuncts to complement existing therapies. In this review, we highlight the role of oncobacteria, specifically those whose relative abundance in the intra-tumour microbiome is increased, and discuss the potential for bacteriophages against these micro-organisms to augment existing cancer therapies. The capacity for bacteriophages to modulate immunity and kill specific bacteria makes them suitable candidates to manipulate the tumour microbiome and negate the effects of these oncobacteria.
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Affiliation(s)
- Mwila Kabwe
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Sharon St. Bendigo, Victoria 3550, Australia
| | - Stuart Dashper
- Melbourne Dental School, University of Melbourne, 720 Swanston St, Parkville, Victoria 3010, Australia
| | - Gilad Bachrach
- The Institute of Dental Sciences, The Hebrew University-Hadassah School of Dental Medicine, PO Box 12272, Jerusalem 9112102, Israel
| | - Joseph Tucci
- Department of Pharmacy and Biomedical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Sharon St. Bendigo, Victoria 3550, Australia
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37
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Bravo-Veyrat S, Hopfgartner G. Mass spectrometry based high-throughput bioanalysis of low molecular weight compounds: are we ready to support personalized medicine? Anal Bioanal Chem 2021; 414:181-192. [PMID: 34424372 PMCID: PMC8748372 DOI: 10.1007/s00216-021-03583-2] [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: 06/02/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 11/18/2022]
Abstract
Liquid chromatography coupled to mass spectrometry (LC-MS) is the gold standard in bioanalysis for the development of quantitative assays to support drug development or therapeutic drug monitoring. High-throughput and low-cost gene sequencing have enabled a paradigm shift from one treatment fits all to personalized medicine (PM). However, gene monitoring provides only partial information about the health state. The full picture requires the combination of gene monitoring with the screening of exogenous compounds, metabolites, lipids, and proteins. This critical review discusses how mass spectrometry–based technologies and approaches including separation sciences, ambient ionization, and ion mobility are/could be used to support high-throughput bioanalysis of endogenous end exogenous low molecular weight compounds. It includes also various biological sample types (from blood to expired air), and various sample preparation techniques.
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Affiliation(s)
- Sophie Bravo-Veyrat
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211, Geneva 4, Switzerland
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry, Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211, Geneva 4, Switzerland.
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Zebrafish Patient-Derived Xenografts Identify Chemo-Response in Pancreatic Ductal Adenocarcinoma Patients. Cancers (Basel) 2021; 13:cancers13164131. [PMID: 34439284 PMCID: PMC8394309 DOI: 10.3390/cancers13164131] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/07/2021] [Accepted: 08/12/2021] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Treating the PDAC (pancreatic ductal adenocarcinoma) zPDXs (zebrafish patient-derived xenografts) with chemotherapy regimens commonly used, we performed a co-clinical trial testing the predictiveness of the model. We found that zPDX may predict patient outcomes, classifying them into responders (R) and non-responders (NR), reporting a statistically significant higher cancer recurrence rate at 1 year after surgery in the NR group: 66.7 versus 14.3%. Our zPDX model seems to be a promising tool for the stratification of PDAC patients. This is a crucial starting point for future study involving more patients to obtain a method to really personalize the oncological treatment of PDAC patients. Abstract It is increasingly evident the necessity of new predictive tools for the treatment of pancreatic ductal adenocarcinoma in a personalized manner. We present a co-clinical trial testing the predictiveness of zPDX (zebrafish patient-derived xenograft) for assessing if patients could benefit from a therapeutic strategy (ClinicalTrials.gov: XenoZ, NCT03668418). zPDX are generated xenografting tumor tissues in zebrafish embryos. zPDX were exposed to chemotherapy regimens commonly used. We considered a zPDX a responder (R) when a decrease ≥50% in the relative tumor area was reported; otherwise, we considered them a non-responder (NR). Patients were classified as Responder if their own zPDX was classified as an R for the chemotherapy scheme she/he received an adjuvant treatment; otherwise, we considered them a Non-Responder. We compared the cancer recurrence rate at 1 year after surgery and the disease-free survival (DFS) of patients of both groups. We reported a statistically significant higher recurrence rate in the Non-Responder group: 66.7% vs. 14.3% (p = 0.036), anticipating relapse/no relapse within 1 year after surgery in 12/16 patients. The mean DFS was longer in the R-group than the NR-group, even if not statistically significant: 19.2 months vs. 12.7 months, (p = 0.123). The proposed strategy could potentially improve preclinical evaluation of treatment modalities and may enable prospective therapeutic selection in everyday clinical practice.
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39
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Dlamini Z, Mbele M, Makhafola TJ, Hull R, Marima R. HIV-Associated Cancer Biomarkers: A Requirement for Early Diagnosis. Int J Mol Sci 2021; 22:ijms22158127. [PMID: 34360891 PMCID: PMC8348540 DOI: 10.3390/ijms22158127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/18/2021] [Accepted: 07/19/2021] [Indexed: 02/07/2023] Open
Abstract
Globally, HIV/AIDS and cancer are increasingly public health problems and continue to exist as comorbidities. The sub-Saharan African region has the largest number of HIV infections. Malignancies previously associated with HIV/AIDS, also known as the AIDS-defining cancers (ADCs) have been documented to decrease, while the non-AIDS defining cancer (NADCs) are on the rise. On the other hand, cancer is a highly heterogeneous disease and precision oncology as the most effective cancer therapy is gaining attraction. Among HIV-infected individuals, the increased risk for developing cancer is due to the immune system of the patient being suppressed, frequent coinfection with oncogenic viruses and an increase in risky behavior such as poor lifestyle. The core of personalised medicine for cancer depends on the discovery and the development of biomarkers. Biomarkers are specific and highly sensitive markers that reveal information that aid in leading to the diagnosis, prognosis and therapy of the disease. This review focuses mainly on the risk assessment, diagnostic, prognostic and therapeutic role of various cancer biomarkers in HIV-positive patients. A careful selection of sensitive and specific HIV-associated cancer biomarkers is required to identify patients at most risk of tumour development, thus improving the diagnosis and prognosis of the disease.
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Knoppers BM, Bernier A, Granados Moreno P, Pashayan N. Of Screening, Stratification, and Scores. J Pers Med 2021; 11:736. [PMID: 34442379 PMCID: PMC8398020 DOI: 10.3390/jpm11080736] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 07/24/2021] [Indexed: 12/16/2022] Open
Abstract
Technological innovations including risk-stratification algorithms and large databases of longitudinal population health data and genetic data are allowing us to develop a deeper understanding how individual behaviors, characteristics, and genetics are related to health risk. The clinical implementation of risk-stratified screening programmes that utilise risk scores to allocate patients into tiers of health risk is foreseeable in the future. Legal and ethical challenges associated with risk-stratified cancer care must, however, be addressed. Obtaining access to the rich health data that are required to perform risk-stratification, ensuring equitable access to risk-stratified care, ensuring that algorithms that perform risk-scoring are representative of human genetic diversity, and determining the appropriate follow-up to be provided to stratification participants to alert them to changes in their risk score are among the principal ethical and legal challenges. Accounting for the great burden that regulatory requirements could impose on access to risk-scoring technologies is another critical consideration.
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Affiliation(s)
- Bartha M. Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, 740 Avenue Dr. Penfield, Suite 5200, Montreal, QC H3A 0G1, Canada; (A.B.); (P.G.M.)
| | - Alexander Bernier
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, 740 Avenue Dr. Penfield, Suite 5200, Montreal, QC H3A 0G1, Canada; (A.B.); (P.G.M.)
| | - Palmira Granados Moreno
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, 740 Avenue Dr. Penfield, Suite 5200, Montreal, QC H3A 0G1, Canada; (A.B.); (P.G.M.)
| | - Nora Pashayan
- Department of Applied Health Research, University College London, 1-19 Torrington Place, London WC1E 7HB, UK;
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Karol D, McKinnon M, Mukhtar L, Awan A, Lo B, Wheatley-Price P. The Impact of Foundation Medicine Testing on Cancer Patients: A Single Academic Centre Experience. Front Oncol 2021; 11:687730. [PMID: 34381713 PMCID: PMC8350441 DOI: 10.3389/fonc.2021.687730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/05/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The use of Next-Generation Sequencing (NGS) has recently allowed significant improvements in cancer treatment. Foundation Medicine® (FM) provides a genomic profiling test based on NGS for a variety of cancers. However, it is unclear if the Foundation Medicine test would result in a better outcome than the standard on-site molecular testing. In this retrospective chart review, we identified the FM cases from an academic Canadian hospital and determined whether these test results improved treatment options for those patients. MATERIALS AND METHODS A retrospective analysis was performed on patients with solid tumors who had FM testing between May 1, 2014 and May 1, 2018. Clinical factors and outcomes were measured using descriptive statistics using Microsoft Excel® Software. RESULTS Out of 66 FM tests, eight patients (= 12%) had a direct change in therapy based on the FM tests. Identified were 285 oncogenic mutations (median 1, range 0-31); where TP53 (n = 31, 10.9%), CDKN2A (n = 19, 6.7%), KRAS (n = 16, 5.6%) and APC (n = 9, 3.2%) were the most common FM mutations identified. CONCLUSION A small proportion of FM reports identified actionable mutations and led to direct treatment change. FM testing is expensive and a few of the identified mutations are now part of routine on-site testing. NGS testing is likely to become more widespread, but this research suggests that its true clinical impact may be restricted to a minority of patients.
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Affiliation(s)
- Dalia Karol
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | | | - Lenah Mukhtar
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Arif Awan
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Medicine, Division of Medical Oncology, The Ottawa Hospital Cancer Centre, Ottawa, ON, Canada
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Bryan Lo
- Department of Anatomical Pathology, The Ottawa Hospital, Ottawa, ON, Canada
| | - Paul Wheatley-Price
- Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Medicine, Division of Medical Oncology, The Ottawa Hospital Cancer Centre, Ottawa, ON, Canada
- The Ottawa Hospital Research Institute, Ottawa, ON, Canada
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Stein MK, Oluoha O, Patel K, VanderWalde A. Precision Medicine in Oncology: A Review of Multi-Tumor Actionable Molecular Targets with an Emphasis on Non-Small Cell Lung Cancer. J Pers Med 2021; 11:518. [PMID: 34198738 PMCID: PMC8226771 DOI: 10.3390/jpm11060518] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 02/07/2023] Open
Abstract
Precision medicine is essential for the modern care of a patient with cancer. Comprehensive molecular profiling of the tumor itself is necessary to determine the presence or absence of certain targetable abnormalities or biomarkers. In particular, lung cancer is a disease for which targetable genomic alterations will soon guide therapy in the majority of cases. In this comprehensive review of solid tumor-based biomarkers, we describe the genomic alterations for which targeted agents have been approved by the United States Food and Drug Administration (FDA). While focusing on alterations leading to approvals in a tumor-agnostic fashion (MSI-h, TMB-h, NTRK) and on those alterations with approvals in multiple malignancies (BRAF, ERBB2, RET, BRCA, PD-L1), we also describe several biomarkers or indications that are likely to lead to an approved drug in the near future (e.g., KRAS G12C, PD-L1 amplification, HER2 overexpression in colon cancer, HER2 mutations in lung cancer). Finally, we detail the current landscape of additional actionable alterations (EGFR, ALK, ROS1, MET) in lung cancer, a biomarker-rich malignancy that has greatly benefitted from the precision oncology revolution.
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Affiliation(s)
- Matthew K. Stein
- Missouri Baptist Medical Center, Heartland Cancer Research, NCI Community Oncology Research Program, St. Louis, MO 63131, USA;
| | - Oluchukwu Oluoha
- Division of Hematology and Oncology, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (O.O.); (K.P.)
| | - Kruti Patel
- Division of Hematology and Oncology, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (O.O.); (K.P.)
| | - Ari VanderWalde
- West Cancer Center and Research Institute, Germantown, TN 38138, USA
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Pennington MW, Zell B, Bai CJ. Commercial manufacturing of current good manufacturing practice peptides spanning the gamut from neoantigen to commercial large-scale products. MEDICINE IN DRUG DISCOVERY 2021. [DOI: 10.1016/j.medidd.2020.100071] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Pires JG, da Silva GF, Weyssow T, Conforte AJ, Pagnoncelli D, da Silva FAB, Carels N. Galaxy and MEAN Stack to Create a User-Friendly Workflow for the Rational Optimization of Cancer Chemotherapy. Front Genet 2021; 12:624259. [PMID: 33679888 PMCID: PMC7935533 DOI: 10.3389/fgene.2021.624259] [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: 10/31/2020] [Accepted: 01/22/2021] [Indexed: 12/24/2022] Open
Abstract
One aspect of personalized medicine is aiming at identifying specific targets for therapy considering the gene expression profile of each patient individually. The real-world implementation of this approach is better achieved by user-friendly bioinformatics systems for healthcare professionals. In this report, we present an online platform that endows users with an interface designed using MEAN stack supported by a Galaxy pipeline. This pipeline targets connection hubs in the subnetworks formed by the interactions between the proteins of genes that are up-regulated in tumors. This strategy has been proved to be suitable for the inhibition of tumor growth and metastasis in vitro. Therefore, Perl and Python scripts were enclosed in Galaxy for translating RNA-seq data into protein targets suitable for the chemotherapy of solid tumors. Consequently, we validated the process of target diagnosis by (i) reference to subnetwork entropy, (ii) the critical value of density probability of differential gene expression, and (iii) the inhibition of the most relevant targets according to TCGA and GDC data. Finally, the most relevant targets identified by the pipeline are stored in MongoDB and can be accessed through the aforementioned internet portal designed to be compatible with mobile or small devices through Angular libraries.
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Affiliation(s)
- Jorge Guerra Pires
- Plataforma de Modelagem de Sistemas Biológicos, Center for Technology Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Gilberto Ferreira da Silva
- Plataforma de Modelagem de Sistemas Biológicos, Center for Technology Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Thomas Weyssow
- Informatic Department, Free University of Brussels (ULB), Brussels, Belgium
| | - Alessandra Jordano Conforte
- Plataforma de Modelagem de Sistemas Biológicos, Center for Technology Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil.,Laboratório de Modelagem Computacional de Sistemas Biológicos, Scientific Computing Program, FIOCRUZ, Rio de Janeiro, Brazil
| | | | - Fabricio Alves Barbosa da Silva
- Laboratório de Modelagem Computacional de Sistemas Biológicos, Scientific Computing Program, FIOCRUZ, Rio de Janeiro, Brazil
| | - Nicolas Carels
- Plataforma de Modelagem de Sistemas Biológicos, Center for Technology Development in Health (CDTS), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
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Rostam Niakan Kalhori S, Tanhapour M, Gholamzadeh M. Enhanced childhood diseases treatment using computational models: Systematic review of intelligent experiments heading to precision medicine. J Biomed Inform 2021; 115:103687. [PMID: 33497811 DOI: 10.1016/j.jbi.2021.103687] [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: 08/31/2020] [Revised: 12/05/2020] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
INTRODUCTION Precision or personalized Medicine (PM) is used for the prevention and treatment of diseases by considering a huge amount of information about individuals variables. Due to high volume of information, AI-based computational models are required. A large set of studies conducted to examine the PM approach to improve childhood clinical outcomes. Thus, the main goal of this study was to review the application of health information technology and especially artificial intelligence (AI) methods for the treatment of childhood disease using PM. METHODS PubMed, Scopus, Web of Science, and EMBASE databases were searched up to December 18, 2019. Articles that focused on informatics applications for childhood disease PM included in this study. Included papers were classified for qualitative analysis and interpreting results. The results were analyzed using Microsoft Excel 2019. RESULTS From 341 citations, 62 papers met our inclusion criteria. The number of published papers that used AI methods to apply for PM in childhood diseases increased from 2010 to 2019. Our results showed that most applied methods were related to machine learning discipline. In terms of clinical scope, the largest number of clinical articles are devoted to oncology. Besides, the analysis showed that genomics was the most PM approach used regarding childhood disease. CONCLUSION This systematic review examined papers that used AI methods for applying PM approaches in childhood diseases from medical informatics perspectives. Thus, it provided new insight to researchers who are interested in knowing research needs in this field.
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Affiliation(s)
- Sharareh Rostam Niakan Kalhori
- Department of Health Information Management, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Mozhgan Tanhapour
- Department of Health Information Management, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Marsa Gholamzadeh
- Department of Health Information Management, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran.
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Sozmen F, Kucukoflaz M, Ergul M, Sahin Inan ZD. Nanoparticles with PDT and PTT synergistic properties working with dual NIR-light source simultaneously. RSC Adv 2021. [DOI: 10.1039/d0ra09954f] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
A non-toxic nano system using a cleverly designed dual light can be an important treatment strategy in cancer therapy.
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Affiliation(s)
- Fazli Sozmen
- Nanotechnology Engineering Department
- Faculty of Engineering
- Sivas Cumhuriyet University
- Sivas
- Turkey
| | - Merve Kucukoflaz
- Nanotechnology Engineering Department
- Faculty of Engineering
- Sivas Cumhuriyet University
- Sivas
- Turkey
| | - Mustafa Ergul
- Biochemistry Department
- Faculty of Pharmacy
- Sivas Cumhuriyet University
- Sivas
- Turkey
| | - Zeynep Deniz Sahin Inan
- Histology and Embryology Department
- Faculty of Medicine
- Sivas Cumhuriyet University
- Sivas
- Turkey
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Mohd Ali N, Yeap SK, Ho WY, Boo L, Ky H, Satharasinghe DA, Tan SW, Cheong SK, Huang HD, Lan KC, Chiew MY, Ong HK. Adipose MSCs Suppress MCF7 and MDA-MB-231 Breast Cancer Metastasis and EMT Pathways Leading to Dormancy via Exosomal-miRNAs Following Co-Culture Interaction. Pharmaceuticals (Basel) 2020; 14:ph14010008. [PMID: 33374139 PMCID: PMC7824212 DOI: 10.3390/ph14010008] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 02/07/2023] Open
Abstract
Globally, breast cancer is the most frequently diagnosed cancer in women, and it remains a substantial clinical challenge due to cancer relapse. The presence of a subpopulation of dormant breast cancer cells that survived chemotherapy and metastasized to distant organs may contribute to relapse. Tumor microenvironment (TME) plays a significant role as a niche in inducing cancer cells into dormancy as well as involves in the reversible epithelial-to-mesenchymal transition (EMT) into aggressive phenotype responsible for cancer-related mortality in patients. Mesenchymal stem cells (MSCs) are known to migrate to TME and interact with cancer cells via secretion of exosome- containing biomolecules, microRNA. Understanding of interaction between MSCs and cancer cells via exosomal miRNAs is important in determining the therapeutic role of MSC in treating breast cancer cells and relapse. In this study, exosomes were harvested from a medium of indirect co-culture of MCF7-luminal and MDA-MB-231-basal breast cancer cells (BCCs) subtypes with adipose MSCs. The interaction resulted in different exosomal miRNAs profiles that modulate essential signaling pathways and cell cycle arrest into dormancy via inhibition of metastasis and epithelial-to-mesenchymal transition (EMT). Overall, breast cancer cells displayed a change towards a more dormant-epithelial phenotype associated with lower rates of metastasis and higher chemoresistance. The study highlights the crucial roles of adipose MSCs in inducing dormancy and identifying miRNAs-dormancy related markers that could be used to identify the metastatic pattern, predict relapses in cancer patients and to be potential candidate targets for new targeted therapy.
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Affiliation(s)
- Norlaily Mohd Ali
- Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Cheras 43000, Malaysia; (N.M.A.); (L.B.); (S.K.C.)
| | - Swee Keong Yeap
- Marine Biotechnology, China-ASEAN College of Marine Sciences, Xiamen University Malaysia Campus, Jalan Sunsuria, Bandar Sunsuria, Sepang, Selangor 43900, Malaysia;
| | - Wan Yong Ho
- Faculty of Medicine and Health Sciences, University of Nottingham (Malaysia Campus), Semenyih 43500, Malaysia;
| | - Lily Boo
- Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Cheras 43000, Malaysia; (N.M.A.); (L.B.); (S.K.C.)
| | - Huynh Ky
- Department of Agriculture Genetics and Breeding, College of Agriculture and Applied Biology, Cantho University, Can Tho 900100, Vietnam;
| | - Dilan Amila Satharasinghe
- Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, Peradeniya 20400, Sri Lanka;
| | - Sheau Wei Tan
- Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Malaysia;
| | - Soon Keng Cheong
- Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Cheras 43000, Malaysia; (N.M.A.); (L.B.); (S.K.C.)
- Cryocord Sdn Bhd, Persiaran Cyberpoint Selatan, Cyberjaya 63000, Malaysia
| | - Hsien Da Huang
- School of Life and Health Sciences, Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China;
| | - Kuan Chun Lan
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu 30010, Taiwan;
| | - Men Yee Chiew
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30010, Taiwan;
| | - Han Kiat Ong
- Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Cheras 43000, Malaysia; (N.M.A.); (L.B.); (S.K.C.)
- Correspondence:
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Hysi E, Fadhel MN, Wang Y, Sebastian JA, Giles A, Czarnota GJ, Exner AA, Kolios MC. Photoacoustic imaging biomarkers for monitoring biophysical changes during nanobubble-mediated radiation treatment. PHOTOACOUSTICS 2020; 20:100201. [PMID: 32775198 PMCID: PMC7393572 DOI: 10.1016/j.pacs.2020.100201] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/24/2020] [Accepted: 07/22/2020] [Indexed: 05/04/2023]
Abstract
The development of novel anticancer therapies warrants the parallel development of biomarkers that can quantify their effectiveness. Photoacoustic imaging has the potential to measure changes in tumor vasculature during treatment. Establishing the accuracy of imaging biomarkers requires direct comparisons with gold histological standards. In this work, we explore whether a new class of submicron, vascular disrupting, ultrasonically stimulated nanobubbles enhance radiation therapy. In vivo experiments were conducted on mice bearing prostate cancer tumors. Combined nanobubble plus radiation treatments were compared against conventional microbubbles and radiation alone (single 8 Gy fraction). Acoustic resolution photoacoustic imaging was used to monitor the effects of the treatments 2- and 24-hs post-administration. Histological examination provided metrics of tumor vascularity and tumoral cell death, both of which were compared to photoacoustic-derived biomarkers. Photoacoustic metrics of oxygen saturation reveal a 20 % decrease in oxygenation within 24 h post-treatment. The spectral slope metric could separate the response of the nanobubble treatments from the microbubble counterparts. This study shows that histopathological assessment correlated well with photoacoustic biomarkers of treatment response.
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Affiliation(s)
- Eno Hysi
- Department of Physics, Ryerson University, Toronto, Canada
- Insitute for Biomedical Engineering, Science and Technology, St. Michael’s Hospital, Toronto, Canada
| | - Muhannad N. Fadhel
- Department of Physics, Ryerson University, Toronto, Canada
- Insitute for Biomedical Engineering, Science and Technology, St. Michael’s Hospital, Toronto, Canada
| | - Yanjie Wang
- Department of Physics, Ryerson University, Toronto, Canada
- Insitute for Biomedical Engineering, Science and Technology, St. Michael’s Hospital, Toronto, Canada
| | - Joseph A. Sebastian
- Department of Physics, Ryerson University, Toronto, Canada
- Insitute for Biomedical Engineering, Science and Technology, St. Michael’s Hospital, Toronto, Canada
| | - Anoja Giles
- Deparment of Radiation Oncology, Sunnybrook Health Sciences Center, Toronto, Canada
- Physical Sciences, Sunnybrook Research Institute, Toronto, Canada
| | - Gregory J. Czarnota
- Deparment of Radiation Oncology, Sunnybrook Health Sciences Center, Toronto, Canada
- Physical Sciences, Sunnybrook Research Institute, Toronto, Canada
- Deparment of Medical Biophysics, University of Toronto, Canada
- Department of Radiation Oncology, University of Toronto, Canada
| | - Agata A. Exner
- Department of Radiology, Case Western Reserve University, Cleveland, United States
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, United States
| | - Michael C. Kolios
- Department of Physics, Ryerson University, Toronto, Canada
- Insitute for Biomedical Engineering, Science and Technology, St. Michael’s Hospital, Toronto, Canada
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Gilazieva Z, Ponomarev A, Rutland C, Rizvanov A, Solovyeva V. Promising Applications of Tumor Spheroids and Organoids for Personalized Medicine. Cancers (Basel) 2020; 12:E2727. [PMID: 32977530 PMCID: PMC7598156 DOI: 10.3390/cancers12102727] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/14/2020] [Accepted: 09/21/2020] [Indexed: 12/12/2022] Open
Abstract
One of the promising directions in personalized medicine is the use of three-dimensional (3D) tumor models such as spheroids and organoids. Spheroids and organoids are three-dimensional cultures of tumor cells that can be obtained from patient tissue and, using high-throughput personalized medicine methods, provide a suitable therapy for that patient. These 3D models can be obtained from most types of tumors, which provides opportunities for the creation of biobanks with appropriate patient materials that can be used to screen drugs and facilitate the development of therapeutic agents. It should be noted that the use of spheroids and organoids would expand the understanding of tumor biology and its microenvironment, help develop new in vitro platforms for drug testing and create new therapeutic strategies. In this review, we discuss 3D tumor spheroid and organoid models, their advantages and disadvantages, and evaluate their promising use in personalized medicine.
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Affiliation(s)
- Zarema Gilazieva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (Z.G.); (A.P.); (A.R.)
| | - Aleksei Ponomarev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (Z.G.); (A.P.); (A.R.)
| | - Catrin Rutland
- Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham NG7 2UH, UK;
| | - Albert Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (Z.G.); (A.P.); (A.R.)
| | - Valeriya Solovyeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia; (Z.G.); (A.P.); (A.R.)
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Metabolic Signaling Cascades Prompted by Glutaminolysis in Cancer. Cancers (Basel) 2020; 12:cancers12092624. [PMID: 32937954 PMCID: PMC7565600 DOI: 10.3390/cancers12092624] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/31/2020] [Accepted: 09/09/2020] [Indexed: 01/09/2023] Open
Abstract
Simple Summary Within the last few years, accumulating evidences suggest the involvement of altered metabolisms in human diseases including cancer. Metabolism is defined as the sum of biochemical processes in living organisms that produce and consume energy. Tumor growth requires restructuring of cellular metabolism to meet the increasing demand for building blocks to support the ever-increasing cancer cell numbers. The principle of perturbed metabolism in tumors is known for 50–60 years, it regains greater appreciation within the last few years with the realization that there is interdependency between metabolism and all aspects of cellular function including regulation and control of cell growth. Tumor cells do not need stimulation signals from the surrounding environment to promote cell proliferation; in some cases, the tumor cells can generate their own growth signals. In order to support the continuous tumor cell growth even under stressful conditions, a change in metabolism is necessary to fulfill the continuous demand for energy and building blocks. A better understanding of the relationship between tumor environment and altered cell metabolisms will provide valuable insights to design innovative approaches to limit the supply of energy and macromolecules for the treatment of cancer including melanoma. Abstract Aberrant glutamatergic signaling has been implicated in altered metabolic activity and the demand to synthesize biomass in several types of cancer including melanoma. In the last decade, there has been a significant contribution to our understanding of metabolic pathways. An increasing number of studies are now emphasizing the importance of glutamate functioning as a signaling molecule and a building block for cancer progression. To that end, our group has previously illustrated the role of glutamatergic signaling mediated by metabotropic glutamate receptor 1 (GRM1) in neoplastic transformation of melanocytes in vitro and spontaneous development of metastatic melanoma in vivo. Glutamate, the natural ligand of GRM1, is one of the most abundant amino acids in humans and the predominant excitatory neurotransmitter in the central nervous system. Elevated levels of glutaminolytic mitochondrial tricarboxylic acid (TCA) cycle intermediates, especially glutamate, have been reported in numerous cancer cells. Herein, we highlight and critically review metabolic bottlenecks that are prevalent during tumor evolution along with therapeutic implications of limiting glutamate bioavailability in tumors.
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