1
|
Guedes A, Nakagawa SA. Biopsy of bone tumors: a literature review. REVISTA DA ASSOCIACAO MEDICA BRASILEIRA (1992) 2024; 70:e2024S131. [PMID: 38865550 PMCID: PMC11164262 DOI: 10.1590/1806-9282.2024s131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/05/2023] [Indexed: 06/14/2024]
Affiliation(s)
- Alex Guedes
- Hospital Santa Izabel, Santa Casa de Misericórdia da Bahia, Orthopedic Oncology Group – Salvador (BA), Brazil
| | - Suely Akiko Nakagawa
- Reference Center for Bone Tumors and Sarcomas, A.C.Camargo Cancer Center – São Paulo (SP), Brazil
| |
Collapse
|
2
|
Chon E, Hendricks W, White M, Rodrigues L, Haworth D, Post G. Precision Medicine in Veterinary Science. Vet Clin North Am Small Anim Pract 2024; 54:501-521. [PMID: 38212188 DOI: 10.1016/j.cvsm.2023.12.006] [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: 01/13/2024]
Abstract
Precision medicine focuses on the clinical management of the individual patient, not on population-based findings. Successes from human precision medicine inform veterinary oncology. Early evidence of success for canines shows how precision medicine can be integrated into practice. Decreasing genomic profiling costs will allow increased utilization and subsequent improvement of knowledge base from which to make better informed decisions. Utility of precision medicine in canine oncology will only increase for improved cancer characterization, enhanced therapy selection, and overall more successful management of canine cancer. As such, practitioners are called to interpret and leverage precision medicine reports for their patients.
Collapse
Affiliation(s)
- Esther Chon
- Vidium Animal Health, 7201 East Henkel Way, Suite 210, Scottsdale, AZ 85255, USA
| | - William Hendricks
- Vidium Animal Health, 7201 East Henkel Way, Suite 210, Scottsdale, AZ 85255, USA
| | - Michelle White
- OneHealthCompany, Inc, 530 Lytton Avenue, 2nd Floor, Palo Alto, CA 94301, USA
| | - Lucas Rodrigues
- OneHealthCompany, Inc, 530 Lytton Avenue, 2nd Floor, Palo Alto, CA 94301, USA
| | - David Haworth
- Vidium Animal Health, 7201 East Henkel Way, Suite 210, Scottsdale, AZ 85255, USA
| | - Gerald Post
- OneHealthCompany, Inc, 530 Lytton Avenue, 2nd Floor, Palo Alto, CA 94301, USA.
| |
Collapse
|
3
|
Singhto N, Pongphitcha P, Jinawath N, Hongeng S, Chutipongtanate S. Extracellular Vesicles for Childhood Cancer Liquid Biopsy. Cancers (Basel) 2024; 16:1681. [PMID: 38730633 PMCID: PMC11083250 DOI: 10.3390/cancers16091681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Liquid biopsy involves the utilization of minimally invasive or noninvasive techniques to detect biomarkers in biofluids for disease diagnosis, monitoring, or guiding treatments. This approach is promising for the early diagnosis of childhood cancer, especially for brain tumors, where tissue biopsies are more challenging and cause late detection. Extracellular vesicles offer several characteristics that make them ideal resources for childhood cancer liquid biopsy. Extracellular vesicles are nanosized particles, primarily secreted by all cell types into body fluids such as blood and urine, and contain molecular cargos, i.e., lipids, proteins, and nucleic acids of original cells. Notably, the lipid bilayer-enclosed structure of extracellular vesicles protects their cargos from enzymatic degradation in the extracellular milieu. Proteins and nucleic acids of extracellular vesicles represent genetic alterations and molecular profiles of childhood cancer, thus serving as promising resources for precision medicine in cancer diagnosis, treatment monitoring, and prognosis prediction. This review evaluates the recent progress of extracellular vesicles as a liquid biopsy platform for various types of childhood cancer, discusses the mechanistic roles of molecular cargos in carcinogenesis and metastasis, and provides perspectives on extracellular vesicle-guided therapeutic intervention. Extracellular vesicle-based liquid biopsy for childhood cancer may ultimately contribute to improving patient outcomes.
Collapse
Affiliation(s)
- Nilubon Singhto
- Ramathibodi Comprehensive Cancer Center, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Pongpak Pongphitcha
- Bangkok Child Health Center, Bangkok Hospital Headquarters, Bangkok 10130, Thailand;
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
- Chakri Naruebodindra Medical Institute, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Samut Prakan 10540, Thailand
- Integrative Computational Biosciences Center, Mahidol University, Nakon Pathom 73170, Thailand
| | - Suradej Hongeng
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Somchai Chutipongtanate
- MILCH and Novel Therapeutics Laboratory, Division of Epidemiology, Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Extracellular Vesicle Working Group, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| |
Collapse
|
4
|
Taghizadeh M, Jafari-Koshki T, Jafarlou V, Raeisi M, Alizadeh L, Roosta Y, Matin S, Jabari R, Sur D, Karimi A. The role of piRNAs in predicting and prognosing in cancer: a focus on piRNA-823 (a systematic review and meta-analysis). BMC Cancer 2024; 24:484. [PMID: 38627675 PMCID: PMC11022431 DOI: 10.1186/s12885-024-12180-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/25/2024] [Indexed: 04/19/2024] Open
Abstract
INTRODUCTION This article examines the potential of using liquid biopsy with piRNAs to study cancer survival outcomes. While previous studies have explored the relationship between piRNA expression and cancer patient outcomes, a comprehensive investigation is still lacking. To address this gap, we conducted a systematic review and meta-analysis of existing literature. METHODS We searched major online databases up to February 2024 to identify articles reporting on the role of piRNA in cancer patient survival outcomes. Our meta-analysis used a random-effects model to pool hazard ratios with 95% confidence intervals (CI) and assess the prognostic value of deregulated piRNA-823. For survival analysis, the Kaplan-Meier method and COX analysis were used. RESULTS Out of 6104 articles screened, 20 met our inclusion criteria. Our analysis revealed that dysregulated piRNA expression is associated with cancer patient survival outcomes. Specifically, our meta-analysis found that overexpression of piR-823 is significantly linked with poorer overall survival in patients with colorectal cancer and renal cell cancer (HR: 3.82, 95% CI = [1.81, 8.04], I2 = 70%). CONCLUSION Our findings suggest that various piRNAs may play a role in cancer survival outcomes and that piRNA-823 in particular holds promise as a prognostic biomarker for multiple human cancers. IMPLICATIONS FOR CANCER SURVIVORS Our systematic review and meta-analysis of piRNA-823 has important implications for cancer survivors. Our findings suggest that piRNA-823 can be used as a prognostic biomarker for predicting cancer recurrence and survival rates. This information can help clinicians develop personalized treatment plans for cancer survivors, which can improve their quality of life and reduce the risk of recurrence.
Collapse
Affiliation(s)
- Mohammad Taghizadeh
- Department of Molecular Medicine, Faculty of Advanced Medical School, Tabriz University of Medical Sciences, Tabriz, 5166614756, Iran
| | - Tohid Jafari-Koshki
- Department of Statistics and Epidemiology, Faculty of Health, Tabriz University of Medical Sciences, Tabriz, 5166616471, Iran
| | - Vahid Jafarlou
- Cancer Institute of Imam Khomeini Hospital, Tehran University of Medical Science, Tehran, 1419733141, Iran
| | - Mortaza Raeisi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, 5166616471, Iran
| | - Leila Alizadeh
- Gastroenterology and Liver Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, 5166616471, Iran
| | - Yousef Roosta
- Department of Internal Medicine, School of Medicine, Urmia University of Medical Sciences, Urmia, 5714783734, Iran
- Solid Tumor Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, 5714783734, Iran
- Hematology, Immune Cell Therapy, and Stem Cells Transplantation Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, 5714783734, Iran
| | - Somaieh Matin
- Department of Internal Medicine, School of Medicine, Ardabil University of Medical Sciences, Ardabil, 8599156189, Iran
| | - Rahele Jabari
- Department of Nutrition Science, Faculty of Medical Science, Urmia University of Medical Science, Urmia, 5714783734, Iran
| | - Daniel Sur
- Department of Oncology, The Oncology Institute "Prof. Dr. Ion Chiricu¸tă", Cluj-Napoca, 400015, Romania.
- Department of Medical Oncology, The Oncology Institute "Prof. Dr. Ion Chiricu ̧t ̆a", 400015 Str. Republicii 34-36, Cluj-Napoca, 400006, Romania.
| | - Abbas Karimi
- Department of Molecular Medicine, Faculty of Advanced Medical School, Tabriz University of Medical Sciences, Tabriz, 5166614756, Iran.
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Golgasht St., Tabriz, East Azerbaijan, 5166614756, Iran.
| |
Collapse
|
5
|
Qu Y, Zhang X, Qiao R, Di F, Song Y, Wang J, Ji L, Zhang J, Gu W, Fang Y, Han B, Yang R, Dai L, Ouyang S. Blood FOLR3 methylation dysregulations and heterogeneity in non-small lung cancer highlight its strong associations with lung squamous carcinoma. Respir Res 2024; 25:59. [PMID: 38273401 PMCID: PMC10809478 DOI: 10.1186/s12931-024-02691-8] [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: 09/30/2023] [Accepted: 01/14/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) accounts for the vast majority of lung cancers. Early detection is crucial to reduce lung cancer-related mortality. Aberrant DNA methylation occurs early during carcinogenesis and can be detected in blood. It is essential to investigate the dysregulated blood methylation markers for early diagnosis of NSCLC. METHODS NSCLC-associated methylation gene folate receptor gamma (FOLR3) was selected from an Illumina 850K array analysis of peripheral blood samples. Mass spectrometry was used for validation in two independent case-control studies (validation I: n = 2548; validation II: n = 3866). Patients with lung squamous carcinoma (LUSC) or lung adenocarcinoma (LUAD), normal controls (NCs) and benign pulmonary nodule (BPN) cases were included. FOLR3 methylations were compared among different populations. Their associations with NSCLC clinical features were investigated. Receiver operating characteristic analyses, Kruskal-Wallis test, Wilcoxon test, logistics regression analysis and nomogram analysis were performed. RESULTS Two CpG sites (CpG_1 and CpG_2) of FOLR3 was significantly lower methylated in NSCLC patients than NCs in the discovery round. In the two validations, both LUSC and LUAD patients presented significant FOLR3 hypomethylations. LUSC patients were highlighted to have significantly lower methylation levels of CpG_1 and CpG_2 than BPN cases and LUAD patients. Both in the two validations, CpG_1 methylation and CpG_2 methylation could discriminate LUSC from NCs well, with areas under the curve (AUCs) of 0.818 and 0.832 in validation I, and 0.789 and 0.780 in validation II. They could also differentiate LUAD from NCs, but with lower efficiency. CpG_1 and CpG_2 methylations could also discriminate LUSC from BPNs well individually in the two validations. With the combined dataset of two validations, the independent associations of age, gender, and FOLR3 methylation with LUSC and LUAD risk were shown and the age-gender-CpG_1 signature could discriminate LUSC and LUAD from NCs and BPNs, with higher efficiency for LUSC. CONCLUSIONS Blood-based FOLR3 hypomethylation was shown in LUSC and LUAD. FOLR3 methylation heterogeneity between LUSC and LUAD highlighted its stronger associations with LUSC. FOLR3 methylation and the age-gender-CpG_1 signature might be novel diagnostic markers for the early detection of NSCLC, especially for LUSC.
Collapse
Affiliation(s)
- Yunhui Qu
- Department of Clinical Laboratory, the First Affiliated Hospital of Zhengzhou University and the Key Clinical Laboratory of Henan Province, Zhengzhou, 450052, China
| | - Xiuzhi Zhang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou, 4500001, China
| | - Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Feifei Di
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Yakang Song
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Jun Wang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China
| | - Longtao Ji
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450052, China
| | - Jie Zhang
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, 210000, China
| | - Yifei Fang
- Department of Respiratory and Sleep Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Rongxi Yang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, 210000, China.
- Department of Epidemiology, School of Public Health, Nanjing Medical University, Nanjing, 210000, China.
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences & Henan Key Medical Laboratory of Tumor Molecular Biomarkers, Zhengzhou University, Zhengzhou, 450052, China.
| | - Songyun Ouyang
- Department of Respiratory and Sleep Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
| |
Collapse
|
6
|
Baran K, Waśko J, Kryczka J, Boncela J, Jabłoński S, Kolesińska B, Brzeziańska-Lasota E, Kordiak J. The Comparison of Serum Exosome Protein Profile in Diagnosis of NSCLC Patients. Int J Mol Sci 2023; 24:13669. [PMID: 37761972 PMCID: PMC10650331 DOI: 10.3390/ijms241813669] [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: 08/10/2023] [Revised: 08/31/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023] Open
Abstract
A thorough study of the exosomal proteomic cargo may enable the identification of proteins that play an important role in cancer development. The aim of this study was to compare the protein profiles of the serum exosomes derived from non-small lung cancer (NSCLC) patients and healthy volunteers (control) using the high-performance liquid chromatography coupled to mass spectrometry (HPLC-MS) method to identify potentially new diagnostic and/or prognostic protein biomarkers. Proteins exclusively identified in NSCLC and control groups were analyzed using several bioinformatic tools and platforms (FunRich, Vesiclepedia, STRING, and TIMER2.0) to find key protein hubs involved in NSCLC progression and the acquisition of metastatic potential. This analysis revealed 150 NSCLC proteins, which are significantly involved in osmoregulation, cell-cell adhesion, cell motility, and differentiation. Among them, 3 proteins: Interleukin-34 (IL-34), HLA class II histocompatibility antigen, DM alpha chain (HLA-DMA), and HLA class II histocompatibility antigen, DO beta chain (HLA-DOB) were shown to be significantly involved in the cancer-associated fibroblasts (CAFs) and tumor-associated macrophages (TAMs) infiltration processes. Additionally, detected proteins were analyzed according to the presence of lymph node metastasis, showing that differences in frequency of detection of protein FAM166B, killer cell immunoglobulin-like receptor 2DL1, and olfactory receptor 52R1 correlate with the N feature according to the TNM Classification of Malignant Tumors. These results prove their involvement in NSCLC lymph node spread and metastasis. However, this study requires further investigation.
Collapse
Affiliation(s)
- Kamila Baran
- Department of Biomedicine and Genetics, Medical University of Lodz, 92-213 Lodz, Poland;
| | - Joanna Waśko
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland; (J.W.); (B.K.)
| | - Jakub Kryczka
- Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.K.); (J.B.)
| | - Joanna Boncela
- Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.K.); (J.B.)
| | - Sławomir Jabłoński
- Department of Thoracic, General and Oncological Surgery, Medical University of Lodz, 90-549 Lodz, Poland; (S.J.); (J.K.)
| | - Beata Kolesińska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland; (J.W.); (B.K.)
| | - Ewa Brzeziańska-Lasota
- Department of Biomedicine and Genetics, Medical University of Lodz, 92-213 Lodz, Poland;
| | - Jacek Kordiak
- Department of Thoracic, General and Oncological Surgery, Medical University of Lodz, 90-549 Lodz, Poland; (S.J.); (J.K.)
| |
Collapse
|
7
|
Qiao R, Di F, Wang J, Wei Y, Xu T, Dai L, Gu W, Han B, Yang R. Identification of FUT7 hypomethylation as the blood biomarker in the prediction of early-stage lung cancer. J Genet Genomics 2023; 50:573-581. [PMID: 36898609 DOI: 10.1016/j.jgg.2023.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 02/09/2023] [Accepted: 02/17/2023] [Indexed: 03/12/2023]
Abstract
Early detection of lung cancer (LC) is vital for reducing LC-related mortality. However, noninvasive diagnostic tools remain a great challenge. We aim to identify blood-based biomarkers for the early detection of LC. Here, LC-associated hypomethylation in alpha-1,3-fucosyltransferase VII (FUT7) is identified via the Illumina 850K array in a discovery study and validated by mass spectrometry in two independent case-control studies with blood samples from 1720 LC patients (86.8% LC at stage I, blood is collected before surgery and treatment) and 3143 healthy controls. Compared to the controls, blood-based FUT7 hypomethylation is identified in LC patients at stage I, and even in LC patients with malignant nodules ≤ 1 cm and in patients with adenocarcinoma in situ. Gender plays a role in the LC-associated FUT7 hypomethylation in blood, which is more significant in males than in females. We also reveal that FUT7 hypomethylation in LC could be enhanced by the advanced stage of cancer, involvement of lymph nodes, and larger tumor size. Based on a large sample size and semi-quantitative methods, our study reveals a strong association between blood-based FUT7 hypomethylation and LC, suggesting that methylation signatures in blood may be a group of potential biomarkers for detection of early-stage LC.
Collapse
Affiliation(s)
- Rong Qiao
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China
| | - Feifei Di
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, Jiangsu 210061, China
| | - Jun Wang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, Jiangsu 210061, China
| | - Yujie Wei
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, Jiangsu 210061, China
| | - Tian Xu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Wanjian Gu
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Nanjing, Jiangsu 210029, China
| | - Baohui Han
- Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China.
| | - Rongxi Yang
- Nanjing TANTICA Biotechnology Co. Ltd, Nanjing, Jiangsu 210061, China; Department of Epidemiology and Biostatistics, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu 211166, China; Department of Genetic Toxicology, The Key Laboratory of Modern Toxicology of Ministry of Education, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu 211166, China.
| |
Collapse
|
8
|
Khaksari S, Abnous K, Hadizadeh F, Ramezani M, Taghdisi SM, Mousavi Shaegh SA. Signal amplification strategies in biosensing of extracellular vesicles (EVs). Talanta 2023; 256:124244. [PMID: 36640707 DOI: 10.1016/j.talanta.2022.124244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 12/25/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
Extracellular vesicles (EVs) are membrane-enclosed vesicles secreted from mammalian cells. EVs act as multicomponent delivery vehicles to carry a wide variety of biological molecular information and participate in intercellular communications. Since elevated levels of EVs are associated with some pathological states such as inflammatory diseases and cancers, probing circulating EVs holds a great potential for early diagnostics. To this end, several detection methods have been developed in which biosensors have attracted great attentions in identification of EVs due to their simple instrumentation, versatile design and portability for point-of-care applications. The concentrations of EVs in bodily fluids are extremely low (i.e. 1-100 per μl) at early stages of a disease, which necessitates the use of signal amplification strategies for EVs detection. In this way, this review presents and discusses various amplification strategies for EVs biosensors based on detection modalities including surface plasmon resonance (SPR), calorimetry, fluorescence, electrochemical and electrochemiluminescence (ECL). In addition, microfluidic systems employed for signal amplification are reviewed and discussed in terms of their design and integration with the detection methods.
Collapse
Affiliation(s)
- Sedighe Khaksari
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Laboratory of Microfluidics and Medical Microsystems, Bu Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Khalil Abnous
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Farzin Hadizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran; Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Ali Mousavi Shaegh
- Orthopedic Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Clinical Research Unit, Mashhad University of Medical Sciences, Mashhad, Iran; Laboratory of Microfluidics and Medical Microsystems, Bu Ali Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
9
|
Li Y, Jiang G, Wu W, Yang H, Jin Y, Wu M, Liu W, Yang A, Chervova O, Zhang S, Zheng L, Zhang X, Du F, Kanu N, Wu L, Yang F, Wang J, Chen K. Multi-omics integrated circulating cell-free DNA genomic signatures enhanced the diagnostic performance of early-stage lung cancer and postoperative minimal residual disease. EBioMedicine 2023; 91:104553. [PMID: 37027928 PMCID: PMC10102814 DOI: 10.1016/j.ebiom.2023.104553] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Liquid biopsy is a promising non-invasive alternative for cancer screening and minimal residual disease (MRD) detection, although there are some concerns regarding its clinical applications. We aimed to develop an accurate detection platform based on liquid biopsy for both cancer screening and MRD detection in patients with lung cancer (LC), which is also applicable to clinical use. METHODS We applied a modified whole-genome sequencing (WGS) -based High-performance Infrastructure For MultIomics (HIFI) method for LC screening and postoperative MRD detection by combining the hyper-co-methylated read approach and the circulating single-molecule amplification and resequencing technology (cSMART2.0). FINDINGS For early screening of LC, the LC score model was constructed using the support vector machine, which showed sensitivity (51.8%) at high specificity (96.3%) and achieved an AUC of 0.912 in the validation set prospectively enrolled from multiple centers. The screening model achieved detection efficiency with an AUC of 0.906 in patients with lung adenocarcinoma and outperformed other clinical models in solid nodule cohort. When applied the HIFI model to real social population, a negative predictive value (NPV) of 99.92% was achieved in Chinese population. Additionally, the MRD detection rate improved significantly by combining results from WGS and cSMART2.0, with sensitivity of 73.7% at specificity of 97.3%. INTERPRETATION In conclusion, the HIFI method is promising for diagnosis and postoperative monitoring of LC. FUNDING This study was supported by CAMS Innovation Fund for Medical Sciences, Chinese Academy of Medical Sciences, National Natural Science Foundation of China, Beijing Natural Science Foundation and Peking University People's Hospital.
Collapse
|
10
|
Brockley LJ, Souza VGP, Forder A, Pewarchuk ME, Erkan M, Telkar N, Benard K, Trejo J, Stewart MD, Stewart GL, Reis PP, Lam WL, Martinez VD. Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer. Cancers (Basel) 2023; 15:2275. [PMID: 37190212 PMCID: PMC10136462 DOI: 10.3390/cancers15082275] [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: 03/07/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Lung cancer detection and monitoring are hampered by a lack of sensitive biomarkers, which results in diagnosis at late stages and difficulty in tracking response to treatment. Recent developments have established liquid biopsies as promising non-invasive methods for detecting biomarkers in lung cancer patients. With concurrent advances in high-throughput sequencing technologies and bioinformatics tools, new approaches for biomarker discovery have emerged. In this article, we survey established and emerging biomarker discovery methods using nucleic acid materials derived from bodily fluids in the context of lung cancer. We introduce nucleic acid biomarkers extracted from liquid biopsies and outline biological sources and methods of isolation. We discuss next-generation sequencing (NGS) platforms commonly used to identify novel biomarkers and describe how these have been applied to liquid biopsy. We highlight emerging biomarker discovery methods, including applications of long-read sequencing, fragmentomics, whole-genome amplification methods for single-cell analysis, and whole-genome methylation assays. Finally, we discuss advanced bioinformatics tools, describing methods for processing NGS data, as well as recently developed software tailored for liquid biopsy biomarker detection, which holds promise for early diagnosis of lung cancer.
Collapse
Affiliation(s)
- Liam J. Brockley
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Vanessa G. P. Souza
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil;
| | - Aisling Forder
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Michelle E. Pewarchuk
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Melis Erkan
- Department of Pathology and Laboratory Medicine, IWK Health Centre, Halifax, NS B3K 6R8, Canada;
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
| | - Nikita Telkar
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
- British Columbia Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Katya Benard
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Jessica Trejo
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Matt D. Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Greg L. Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Patricia P. Reis
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil;
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
| | - Wan L. Lam
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada; (V.G.P.S.); (A.F.); (M.E.P.); (N.T.); (K.B.); (J.T.); (M.D.S.); (G.L.S.); (W.L.L.)
| | - Victor D. Martinez
- Department of Pathology and Laboratory Medicine, IWK Health Centre, Halifax, NS B3K 6R8, Canada;
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
| |
Collapse
|
11
|
Clack K, Soda N, Kasetsirikul S, Mahmudunnabi RG, Nguyen NT, Shiddiky MJA. Toward Personalized Nanomedicine: The Critical Evaluation of Micro and Nanodevices for Cancer Biomarker Analysis in Liquid Biopsy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205856. [PMID: 36631277 DOI: 10.1002/smll.202205856] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Liquid biopsy for the analysis of circulating cancer biomarkers (CBs) is a major advancement toward the early detection of cancer. In comparison to tissue biopsy techniques, liquid biopsy is relatively painless, offering multiple sampling opportunities across easily accessible bodily fluids such as blood, urine, and saliva. Liquid biopsy is also relatively inexpensive and simple, avoiding the requirement for specialized laboratory equipment or trained medical staff. Major advances in the field of liquid biopsy are attributed largely to developments in nanotechnology and microfabrication that enables the creation of highly precise chip-based platforms. These devices can overcome detection limitations of an individual biomarker by detecting multiple markers simultaneously on the same chip, or by featuring integrated and combined target separation techniques. In this review, the major advances in the field of portable and semi-portable micro, nano, and multiplexed platforms for CB detection for the early diagnosis of cancer are highlighted. A comparative discussion is also provided, noting merits and drawbacks of the platforms, especially in terms of portability. Finally, key challenges toward device portability and possible solutions, as well as discussing the future direction of the field are highlighted.
Collapse
Affiliation(s)
- Kimberley Clack
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Narshone Soda
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Surasak Kasetsirikul
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Rabbee G Mahmudunnabi
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science (ESC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
- Queensland Micro and Nanotechnology Centre (QMNC), Griffith University, Nathan Campus, Nathan, QLD, 4111, Australia
| |
Collapse
|
12
|
Zheng F, Wang J, Wang D, Yang Q. Clinical Application of Small Extracellular Vesicles in Gynecologic Malignancy Treatments. Cancers (Basel) 2023; 15:cancers15071984. [PMID: 37046644 PMCID: PMC10093031 DOI: 10.3390/cancers15071984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Small extracellular vesicles (sEVs) are the key mediators of intercellular communication. They have the potential for clinical use as diagnostic or therapeutic biomarkers and have been explored as vectors for drug delivery. Identification of reliable and noninvasive biomarkers, such as sEVs, is important for early diagnosis and precise treatment of gynecologic diseases to improve patient prognosis. Previous reviews have summarized routine sEVs isolation and identification methods; however, novel and unconventional methods have not been comprehensively described. This review summarizes a convenient method of isolating sEVs from body fluids and liquid biopsy-related sEV markers for early, minimally invasive diagnosis of gynecologic diseases. In addition, the characteristics of sEVs as drug carriers and in precision treatment and drug resistance are introduced, providing a strong foundation for identifying novel and potential therapeutic targets for sEV therapy. We propose potential directions for further research on the applications of sEVs in the diagnosis and treatment of gynecologic diseases.
Collapse
|
13
|
Einoch Amor R, Levy J, Broza YY, Vangravs R, Rapoport S, Zhang M, Wu W, Leja M, Behar JA, Haick H. Liquid Biopsy-Based Volatile Organic Compounds from Blood and Urine and Their Combined Data Sets for Highly Accurate Detection of Cancer. ACS Sens 2023; 8:1450-1461. [PMID: 36926819 DOI: 10.1021/acssensors.2c02422] [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: 03/18/2023]
Abstract
Liquid biopsy is seen as a prospective tool for cancer screening and tracking. However, the difficulty lies in effectively sieving, isolating, and overseeing cancer biomarkers from the backdrop of multiple disrupting cells and substances. The current study reports on the ability to perform liquid biopsy without the need to physically filter and/or isolate the cancer cells per se. This has been achieved through the detection and classification of volatile organic compounds (VOCs) emitted from the cancer cells found in the headspace of blood or urine samples or a combined data set of both. Spectrometric analysis shows that blood and urine contain complementary or overlapping VOC information on kidney cancer, gastric cancer, lung cancer, and fibrogastroscopy subjects. Based on this information, a nanomaterial-based chemical sensor array in conjugation with machine learning as well as data fusion of the signals achieved was carried out on various body fluids to assess the VOC profiles of cancer. The detection of VOC patterns by either Gas Chromatography-Mass Spectrometry (GC-MS) analysis or our sensor array achieved >90% accuracy, >80% sensitivity, and >80% specificity in different binary classification tasks. The hybrid approach, namely, analyzing the VOC datasets of blood and urine together, contributes an additional discrimination ability to the improvement (>3%) of the model's accuracy. The contribution of the hybrid approach for an additional discrimination ability to the improvement of the model's accuracy is examined and reported.
Collapse
Affiliation(s)
- Reef Einoch Amor
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Jeremy Levy
- The Andrew and Erna Viterbi Faculty of Electrical & Computer Engineering and Faculty of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Yoav Y Broza
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Reinis Vangravs
- Institute of Clinical and Preventive Medicine & Faculty of Medicine, University of Latvia, Riga LV-1004, Latvia.,Department of Research, Riga East University Hospital, Digestive Diseases Centre GASTRO, Riga 1586, Latvia
| | - Shelley Rapoport
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Min Zhang
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, Shanghai 200241, China
| | - Weiwei Wu
- School of Advanced Materials and Nanotechnology, Interdisciplinary Research Center of Smart Sensors, Xidian University, Shaanxi 710126, P.R. China
| | - Marcis Leja
- Institute of Clinical and Preventive Medicine & Faculty of Medicine, University of Latvia, Riga LV-1004, Latvia.,Department of Research, Riga East University Hospital, Digestive Diseases Centre GASTRO, Riga 1586, Latvia
| | - Joachim A Behar
- The Andrew and Erna Viterbi Faculty of Electrical & Computer Engineering and Faculty of Biomedical Engineering, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Hossam Haick
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| |
Collapse
|
14
|
Casagrande GMS, Silva MDO, Reis RM, Leal LF. Liquid Biopsy for Lung Cancer: Up-to-Date and Perspectives for Screening Programs. Int J Mol Sci 2023; 24:2505. [PMID: 36768828 PMCID: PMC9917347 DOI: 10.3390/ijms24032505] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 01/31/2023] Open
Abstract
Lung cancer is the deadliest cancer worldwide. Tissue biopsy is currently employed for the diagnosis and molecular stratification of lung cancer. Liquid biopsy is a minimally invasive approach to determine biomarkers from body fluids, such as blood, urine, sputum, and saliva. Tumor cells release cfDNA, ctDNA, exosomes, miRNAs, circRNAs, CTCs, and DNA methylated fragments, among others, which can be successfully used as biomarkers for diagnosis, prognosis, and prediction of treatment response. Predictive biomarkers are well-established for managing lung cancer, and liquid biopsy options have emerged in the last few years. Currently, detecting EGFR p.(Tyr790Met) mutation in plasma samples from lung cancer patients has been used for predicting response and monitoring tyrosine kinase inhibitors (TKi)-treated patients with lung cancer. In addition, many efforts continue to bring more sensitive technologies to improve the detection of clinically relevant biomarkers for lung cancer. Moreover, liquid biopsy can dramatically decrease the turnaround time for laboratory reports, accelerating the beginning of treatment and improving the overall survival of lung cancer patients. Herein, we summarized all available and emerging approaches of liquid biopsy-techniques, molecules, and sample type-for lung cancer.
Collapse
Affiliation(s)
| | - Marcela de Oliveira Silva
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331 Rua Antenor Duarte Vilela, Barretos 14784-400, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331 Rua Antenor Duarte Vilela, Barretos 14784-400, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, Campus de Gualtar, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Letícia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, 1331 Rua Antenor Duarte Vilela, Barretos 14784-400, Brazil
- Barretos School of Medicine Dr. Paulo Prata—FACISB, Barretos 14785-002, Brazil
| |
Collapse
|
15
|
Styk J, Pös Z, Pös O, Radvanszky J, Turnova EH, Buglyó G, Klimova D, Budis J, Repiska V, Nagy B, Szemes T. Microsatellite instability assessment is instrumental for Predictive, Preventive and Personalised Medicine: status quo and outlook. EPMA J 2023; 14:143-165. [PMID: 36866160 PMCID: PMC9971410 DOI: 10.1007/s13167-023-00312-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/06/2023] [Indexed: 01/26/2023]
Abstract
A form of genomic alteration called microsatellite instability (MSI) occurs in a class of tandem repeats (TRs) called microsatellites (MSs) or short tandem repeats (STRs) due to the failure of a post-replicative DNA mismatch repair (MMR) system. Traditionally, the strategies for determining MSI events have been low-throughput procedures that typically require assessment of tumours as well as healthy samples. On the other hand, recent large-scale pan-tumour studies have consistently highlighted the potential of massively parallel sequencing (MPS) on the MSI scale. As a result of recent innovations, minimally invasive methods show a high potential to be integrated into the clinical routine and delivery of adapted medical care to all patients. Along with advances in sequencing technologies and their ever-increasing cost-effectiveness, they may bring about a new era of Predictive, Preventive and Personalised Medicine (3PM). In this paper, we offered a comprehensive analysis of high-throughput strategies and computational tools for the calling and assessment of MSI events, including whole-genome, whole-exome and targeted sequencing approaches. We also discussed in detail the detection of MSI status by current MPS blood-based methods and we hypothesised how they may contribute to the shift from conventional medicine to predictive diagnosis, targeted prevention and personalised medical services. Increasing the efficacy of patient stratification based on MSI status is crucial for tailored decision-making. Contextually, this paper highlights drawbacks both at the technical level and those embedded deeper in cellular/molecular processes and future applications in routine clinical testing.
Collapse
Affiliation(s)
- Jakub Styk
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia ,Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia
| | - Zuzana Pös
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Institute of Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Ondrej Pös
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia
| | - Jan Radvanszky
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Institute of Clinical and Translational Research, Biomedical Research Centre, Slovak Academy of Sciences, 845 05 Bratislava, Slovakia ,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
| | - Evelina Hrckova Turnova
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Slovgen Ltd, 841 04 Bratislava, Slovakia
| | - Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Daniela Klimova
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
| | - Jaroslav Budis
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Slovak Centre of Scientific and Technical Information, 811 04 Bratislava, Slovakia
| | - Vanda Repiska
- Institute of Medical Biology, Genetics and Clinical Genetics, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia ,Medirex Group Academy, NPO, 949 05 Nitra, Slovakia
| | - Bálint Nagy
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Department of Human Genetics, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary
| | - Tomas Szemes
- Comenius University Science Park, 841 04 Bratislava, Slovakia ,Geneton Ltd, 841 04 Bratislava, Slovakia ,Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 841 04 Bratislava, Slovakia
| |
Collapse
|
16
|
Pabico LJ, Jaron JN, Mosqueda ME, Wu JJ, Tiongco RE, Albano PM. Diagnostic Efficiency of Serum-Based Infrared Spectroscopy in Detecting Breast Cancer: A Meta-Analysis. Lab Med 2023; 54:98-105. [PMID: 35960788 DOI: 10.1093/labmed/lmac068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The advancement of Fourier transform infrared (FTIR) spectroscopy as a potential diagnostic tool in the clinical setting has been studied over the years, particularly its application in cancer diagnostics. OBJECTIVE To summarize previous research on FTIR spectroscopy in detecting breast cancer using serum specimens. METHODS Related literature was searched and screened from various databases. Relevant data were then extracted, tabulated, and analyzed using Meta-DiSc 1.4 software. RESULTS Sensitivity and specificity rates were 90% to 100% and 80% to 95%, respectively. The area under the receiver operating characteristic curve was at 0.9729, indicating that serum analysis via FTIR spectroscopy can accurately discriminate between healthy individuals and patients with breast cancer. CONCLUSION Overall, FTIR spectroscopy for breast cancer diagnosis using serum specimens shows promising results. However, further studies are still needed to validate these claims.
Collapse
Affiliation(s)
- Louise Julie Pabico
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Jennica Naiomi Jaron
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Marc Erickson Mosqueda
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Jorge Jaesen Wu
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Raphael Enrique Tiongco
- Department of Medical Technology, College of Allied Medical Professions, Angeles University Foundation, Angeles City, Philippines
| | - Pia Marie Albano
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines.,Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| |
Collapse
|
17
|
Paramanantham A, Asfiya R, Das S, McCully G, Srivastava A. Extracellular Vesicle (EVs) Associated Non-Coding RNAs in Lung Cancer and Therapeutics. Int J Mol Sci 2022; 23:13637. [PMID: 36362424 PMCID: PMC9655370 DOI: 10.3390/ijms232113637] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 10/26/2022] [Indexed: 08/13/2023] Open
Abstract
Lung cancer is one of the most lethal forms of cancer, with a very high mortality rate. The precise pathophysiology of lung cancer is not well understood, and pertinent information regarding the initiation and progression of lung cancer is currently a crucial area of scientific investigation. Enhanced knowledge about the disease will lead to the development of potent therapeutic interventions. Extracellular vesicles (EVs) are membrane-bound heterogeneous populations of cellular entities that are abundantly produced by all cells in the human body, including the tumor cells. A defined class of EVs called small Extracellular Vesicles (sEVs or exosomes) carries key biomolecules such as RNA, DNA, Proteins and Lipids. Exosomes, therefore, mediate physiological activities and intracellular communication between various cells, including constituent cells of the tumor microenvironment, namely stromal cells, immunological cells, and tumor cells. In recent years, a surge in studying tumor-associated non-coding RNAs (ncRNAs) has been observed. Subsequently, studies have also reported that exosomes abundantly carry different species of ncRNAs and these exosomal ncRNAs are functionally involved in cancer initiation and progression. Here, we discuss the function of exosomal ncRNAs, such as miRNAs and long non-coding RNAs, in the pathophysiology of lung tumors. Further, the future application of exosomal-ncRNAs in clinics as biomarkers and therapeutic targets in lung cancer is also discussed due to the multifaceted influence of exosomes on cellular physiology.
Collapse
Affiliation(s)
- Anjugam Paramanantham
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Rahmat Asfiya
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Siddharth Das
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Grace McCully
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
| | - Akhil Srivastava
- Department of Pathology and Anatomical Sciences, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, MO 65212, USA
| |
Collapse
|
18
|
Palmieri M, Zulato E, Wahl SGF, Guibert N, Frullanti E. Diagnostic accuracy of circulating free DNA testing for the detection of KRAS mutations in non-small cell lung cancer: A systematic review and meta-analysis. Front Genet 2022; 13:1015161. [PMID: 36386815 PMCID: PMC9640997 DOI: 10.3389/fgene.2022.1015161] [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: 08/09/2022] [Accepted: 10/11/2022] [Indexed: 11/25/2022] Open
Abstract
Kirsten rat sarcoma viral oncogene homolog (KRAS) gene encodes a GTPase that acts as a molecular switch for intracellular signal transduction, promoting cell growth and proliferation. Mutations in the KRAS gene represent important biomarkers for NSCLC targeted therapy. However, detection of KRAS mutations in tissues has shown some limitations. During the last years, analyses of circulating free DNA (cfDNA) has emerged as an alternative and minimally invasive, approach to investigate tumor molecular changes. Here, we assessed the diagnostic performance of cfDNA analysis, compared to tissues through a meta-analysis and systematic review of existing literature. From 561 candidate papers, we finally identified 40 studies, including 2,805 NSCLC patients. We extracted values relating to the number of true-positive, false-positive, false-negative, and true-negative. Pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio, each with 95% CI, were calculated. A summary receiver operating characteristic curve and the area under curve (AUC) were used to evaluate the overall diagnostic performance. The pooled sensitivity was 0.71 (95% CI 0.68–0.74) and the specificity was 0.93 (95% CI 0.92–0.94). The diagnostic odds ratio was 35.24 (95% CI 24.88–49.91) and the area under the curve was 0.92 (SE = 0.094). These results provide evidence that detection of KRAS mutation using cfDNA testing is of adequate diagnostic accuracy thus offering to the clinicians a new promising screening test for NSCLC patients.
Collapse
Affiliation(s)
- Maria Palmieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Elisabetta Zulato
- Basic and Translational Oncology Unit, Istituto Oncologico Veneto IOV—IRCCS, Padova, Italy
| | - Sissel Gyrid Freim Wahl
- Department of Pathology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, NTNU, Norwegian University of Technology and Science, Trondheim, Norway
| | - Nicolas Guibert
- Thoracic Oncology Department, Larrey Hospital, University Hospital of Toulouse, Toulouse, France
- Inserm, Centre de Recherche en Cancérologie de Toulouse, CRCT UMR-1037, Toulouse, France
- University of Toulouse III (Paul Sabatier), Toulouse, France
| | - Elisa Frullanti
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- *Correspondence: Elisa Frullanti,
| |
Collapse
|
19
|
Einoch Amor R, Zinger A, Broza YY, Schroeder A, Haick H. Artificially Intelligent Nanoarray Detects Various Cancers by Liquid Biopsy of Volatile Markers. Adv Healthc Mater 2022; 11:e2200356. [PMID: 35765713 DOI: 10.1002/adhm.202200356] [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: 02/14/2022] [Revised: 05/24/2022] [Indexed: 01/27/2023]
Abstract
Cancer is usually not symptomatic in its early stages. However, early detection can vastly improve prognosis. Liquid biopsy holds great promise for early detection, although it still suffers from many disadvantages, mainly searching for specific cancer biomarkers. Here, a new approach for liquid biopsies is proposed, based on volatile organic compound (VOC) patterns in the blood headspace. An artificial intelligence nanoarray based on a varied set of chemi-sensitive nano-based structured films is developed and used to detect and stage cancer. As a proof-of-concept, three cancer models are tested showing high incidence and mortality rates in the population: breast cancer, ovarian cancer, and pancreatic cancer. The nanoarray has >84% accuracy, >81% sensitivity, and >80% specificity for early detection and >97% accuracy, 100% sensitivity, and >88% specificity for metastasis detection. Complementary mass spectrometry analysis validates these results. The ability to analyze such a complex biological fluid as blood, while considering data of many VOCs at a time using the artificially intelligent nanoarray, increases the sensitivity of predictive models and leads to a potential efficient early diagnosis and disease-monitoring tool for cancer.
Collapse
Affiliation(s)
- Reef Einoch Amor
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Assaf Zinger
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Yoav Y Broza
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Avi Schroeder
- Laboratory for Targeted Drug Delivery and Personalized Medicine Technologies, Department of Chemical Engineering, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Hossam Haick
- Department of Chemical Engineering and Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| |
Collapse
|
20
|
Chantre-Justino M, Alves G, Delmonico L. Clinical applications of liquid biopsy in HPV‐negative and HPV‐positive head and neck squamous cell carcinoma: advances and challenges. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2022; 3:533-552. [PMID: 36071985 PMCID: PMC9446158 DOI: 10.37349/etat.2022.00099] [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: 04/21/2022] [Accepted: 06/22/2022] [Indexed: 12/02/2022] Open
Abstract
Head and neck squamous cell carcinomas (HNSCCs) represent the most common epithelial tumors that arise from mucosa of the oral cavity, pharynx, and larynx. The development of HNSCCs is usually associated with tobacco use, alcohol consumption, and human papillomavirus (HPV) infection. Most HNSCCs are diagnosed in advanced states, leading to a worse clinical outcome. Screening tests based on potential biomarkers associated with HNSCCs could improve this scenario. Liquid biopsy has emerged as a promising area of cancer investigation, offering a minimally invasive approach to track circulating biomarkers in body fluids that could potentially contribute to the diagnosis, predict prognosis, and monitor response to treatment. This review will discuss translational studies describing the clinical applications of liquid biopsy in HPV-negative and HPV-positive HNSCCs focused on circulating nucleic acids [cell-free DNA (cfDNA) and cell-free RNA (cfRNA)], circulating tumor cells (CTCs), and extracellular vesicles (EVs), which can be found in plasma, serum, and saliva.
Collapse
Affiliation(s)
- Mariana Chantre-Justino
- 1Research Division, National Institute of Traumatology and Orthopaedics (INTO), Rio de Janeiro 20940-070, Brazil 2Circulating Biomarkers Laboratory, Pathology Department, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | - Gilda Alves
- 2Circulating Biomarkers Laboratory, Pathology Department, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | - Lucas Delmonico
- 3Oncoclínicas Precision Medicine, Vila Nova Conceição, São Paulo 04513-020, Brazil
| |
Collapse
|
21
|
Chen J, Oudeng G, Feng H, Liu S, Li HW, Ho YP, Chen Y, Tan Y, Yang M. 2D MOF Nanosensor-Integrated Digital Droplet Microfluidic Flow Cytometry for In Situ Detection of Multiple miRNAs in Single CTC Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2201779. [PMID: 35835723 DOI: 10.1002/smll.202201779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Current circulating tumor cells (CTCs) detection strategies based on surface epithelial markers suffer from low specificity in distinguishing between CTCs and epithelial cells in hematopoietic cell population. Tumor-associated miRNAs within CTCs are emerging as new biomarkers due to their high correlation with tumor development and progress. However, in-situ simultaneous analysis of multiple miRNAs in single CTC cell is still challenging. To overcome this limitation, a digital droplet microfluidic flow cytometry based on biofunctionalized 2D metal-organic framework nanosensor (Nano-DMFC) is developed for in situ detection of dual miRNAs simultaneously in single living breast cancer cells. Here, 2D MOF-based fluorescent resonance energy transfer (FRET) nanosensors are established by conjugating dual-color fluorescence dye-labeled DNA probes on MOF nanosheet surface. In the Nano-DMFC, 2D MOF-based nanoprobes are precisely microinjected into each single-cell encapsulated droplets to achieve dual miRNA characterization in single cancer cell. This Nano-DMFC platform successfully detects dual miRNAs at single-cell resolution in 10 mixed positive MCF-7 cells out of 10 000 negative epithelial cells in serum biomimic samples. Moreover, this Nano-DMFC platform shows good reproductivity in the recovery experiment of spiked blood samples, which demonstrate the high potential for CTC-based cancer early diagnosis and prognosis.
Collapse
Affiliation(s)
- Junyue Chen
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
- Institute of Chemical and Bioengineering, ETH Zurich, Zurich, 8093, Switzerland
| | - Gerile Oudeng
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Futian, Shenzhen, Guangdong, 518026, P. R. China
- Department of Biomedical Engineering, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, 999077, P. R. China
| | - Hongtao Feng
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Sixi Liu
- Department of Hematology and Oncology, Shenzhen Children's Hospital, Futian, Shenzhen, Guangdong, 518026, P. R. China
| | - Hung-Wing Li
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Yi-Ping Ho
- Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, 999077, P. R. China
| | - Yan Chen
- CAS Key Laboratory of Health Informatics, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, P. R. China
| | - Ying Tan
- State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Biology, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, P. R. China
| | - Mo Yang
- Department of Biomedical Engineering, Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong SAR, 999077, P. R. China
| |
Collapse
|
22
|
Kapeleris J, Müller Bark J, Ranjit S, Irwin D, Hartel G, Warkiani ME, Leo P, O'Leary C, Ladwa R, O'Byrne K, Hughes BGM, Punyadeera C. Prognostic value of integrating circulating tumour cells and cell-free DNA in non-small cell lung cancer. Heliyon 2022; 8:e09971. [PMID: 35874074 PMCID: PMC9305346 DOI: 10.1016/j.heliyon.2022.e09971] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/11/2022] [Accepted: 07/13/2022] [Indexed: 11/30/2022] Open
Abstract
Background Non-small cell lung cancer (NSCLC) often presents at an incurable stage, and majority of patients will be considered for palliative treatment at some point in their disease. Despite recent advances, the prognosis remains poor, with a median overall survival of 12–18 months. Liquid biopsy-based biomarkers have emerged as potential candidates for predicting prognosis and response to therapy in NSCLC patients. This pilot study evaluated whether combining circulating tumour cells and clusters (CTCs) and cell-free DNA (cfDNA) can predict progression-free survival (PFS) in NSCLC patients. Methods CTC and cfDNA/ctDNA from advanced stage NSCLC patients were measured at study entry (T0) and 3-months post-treatment (T1). CTCs were enriched using a spiral microfluidic chip and characterised by immunofluorescence. ctDNA was assessed using an UltraSEEK® Lung Panel. Kaplan-Meier plots were generated to investigate the contribution of the presence of CTC/CTC clusters and cfDNA for PFS. Cox proportional hazards analysis compared time to progression versus CTC/CTC cluster counts and cfDNA levels. Results Single CTCs were found in 14 out of 25 patients, while CTC clusters were found in 8 out of the 25 patients at T0. At T1, CTCs were found in 7 out of 18 patients, and CTC clusters in 1 out of the 18 patients. At T0, CTC presence and the combination of CTC cluster counts with cfDNA levels were associated with shorter PFS, p = 0.0261, p = 0.0022, respectively. Conclusions Combining CTC cluster counts and cfDNA levels could improve PFS assessment in NSCLC patients. Our results encourage further investigation on the combined effect of CTC/cfDNA as a prognostic biomarker in a large cohort of advanced stage NSCLC patients.
Collapse
Affiliation(s)
- Joanna Kapeleris
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Centre for Biomedical Technologies, Saliva and Liquid Biopsy Translational Laboratory Kelvin Grove, QLD, Australia.,Translational Research Institute, Woolloongabba, Brisbane, Australia
| | - Juliana Müller Bark
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Centre for Biomedical Technologies, Saliva and Liquid Biopsy Translational Laboratory Kelvin Grove, QLD, Australia.,Translational Research Institute, Woolloongabba, Brisbane, Australia.,Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - Shanon Ranjit
- Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Centre for Biomedical Technologies, Saliva and Liquid Biopsy Translational Laboratory Kelvin Grove, QLD, Australia
| | - Darryl Irwin
- Agena Biosciences, Bowen Hills, Brisbane, QLD, Australia
| | - Gunter Hartel
- QIMR Berghofer Medical Research Institute, Herston Road, Herston, QLD, Australia
| | - Majid Ebrahimi Warkiani
- School of Biomedical Engineering, University of Technology Sydney, Sydney, Ultimo NSW, Australia
| | - Paul Leo
- Translational Research Institute, Woolloongabba, Brisbane, Australia.,Australian Translational Genomics Centre, Queensland University of Technology, Faculty of Health, School of Biomedical Sciences, Woolloongabba, Australia
| | - Connor O'Leary
- Translational Research Institute, Woolloongabba, Brisbane, Australia.,Department of Medical Oncology, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Rahul Ladwa
- Department of Medical Oncology, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia.,School of Medicine, University of Queensland, Herston, Brisbane, Queensland, Australia
| | - Kenneth O'Byrne
- Translational Research Institute, Woolloongabba, Brisbane, Australia.,Department of Medical Oncology, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
| | - Brett G M Hughes
- School of Medicine, University of Queensland, Herston, Brisbane, Queensland, Australia.,The Royal Brisbane and Women's Hospital, Herston, Brisbane, Queensland, Australia
| | - Chamindie Punyadeera
- Translational Research Institute, Woolloongabba, Brisbane, Australia.,Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery, Griffith University, Brisbane, Australia.,Menzies Health Institute, Griffith University, Gold-Coast, Australia
| |
Collapse
|
23
|
Human Blood Platelets Adsorption on Polymeric Materials for Liquid Biopsy. SENSORS 2022; 22:s22134788. [PMID: 35808284 PMCID: PMC9269204 DOI: 10.3390/s22134788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/20/2022] [Accepted: 06/23/2022] [Indexed: 12/04/2022]
Abstract
Platelets are emerging as a promising source of blood biomarkers for several pathologies, including cancer. New automated techniques for easier manipulation of platelets in the context of lab-on-a-chips could be of great support for liquid biopsy. Here, several polymeric materials were investigated for their behavior in terms of adhesion and activation of human platelets. Polymeric materials were selected among the most used in microfabrication (PDMS, PMMA and COC) and commercial and home-made resins for 3D printing technology with the aim to identify the most suitable for the realization of microdevices for human platelets isolation and analysis. To visualize adherent platelets and their activation state scanning, electron microscopy was used, while confocal microscopy was used for evaluating platelets’ features. In addition, atomic force microscopy was employed to further study platelets adherent to the polymeric materials. Polymers were divided in two main groups: the most prone to platelet adhesion and materials that cause few or no platelets to adhere. Therefore, different polymeric materials could be identified as suitable for the realization of microdevices aimed at capturing human platelets, while other materials could be employed for the fabrication of microdevices or parts of microdevices for the processing of platelets, without loss on surfaces during the process.
Collapse
|
24
|
Zambianchi P, Hermógenes G, Zambianchi J. Quantification of gold nanoparticles using total reflection X-ray fluorescence by Monte Carlo simulation (MCNP code) applied to cancer cell research. Radiat Phys Chem Oxf Engl 1993 2022. [DOI: 10.1016/j.radphyschem.2021.109937] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
25
|
Fatima S, Ma Y, Safrachi A, Haider S, Spring KJ, Vafaee F, Scott KF, Roberts TL, Becker TM, de Souza P. Harnessing Liquid Biopsies to Guide Immune Checkpoint Inhibitor Therapy. Cancers (Basel) 2022; 14:1669. [PMID: 35406441 PMCID: PMC8997025 DOI: 10.3390/cancers14071669] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 12/24/2022] Open
Abstract
Immunotherapy (IO), involving the use of immune checkpoint inhibition, achieves improved response-rates and significant disease-free survival for some cancer patients. Despite these beneficial effects, there is poor predictability of response and substantial rates of innate or acquired resistance, resulting in heterogeneous responses among patients. In addition, patients can develop life-threatening adverse events, and while these generally occur in patients that also show a tumor response, these outcomes are not always congruent. Therefore, predicting a response to IO is of paramount importance. Traditionally, tumor tissue analysis has been used for this purpose. However, minimally invasive liquid biopsies that monitor changes in blood or other bodily fluid markers are emerging as a promising cost-effective alternative. Traditional biomarkers have limitations mainly due to difficulty in repeatedly obtaining tumor tissue confounded also by the spatial and temporal heterogeneity of tumours. Liquid biopsy has the potential to circumvent tumor heterogeneity and to help identifying patients who may respond to IO, to monitor the treatment dynamically, as well as to unravel the mechanisms of relapse. We present here a review of the current status of molecular markers for the prediction and monitoring of IO response, focusing on the detection of these markers in liquid biopsies. With the emerging improvements in the field of liquid biopsy, this approach has the capacity to identify IO-eligible patients and provide clinically relevant information to assist with their ongoing disease management.
Collapse
Affiliation(s)
- Shadma Fatima
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2031, Australia; (A.S.); (F.V.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Yafeng Ma
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- South Western Sydney Clinical School, UNSW, Sydney, NSW 2031, Australia
- Centre for Circulating Tumor Cell Diagnosis and Research, Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Azadeh Safrachi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2031, Australia; (A.S.); (F.V.)
| | - Sana Haider
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Kevin J. Spring
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2031, Australia; (A.S.); (F.V.)
- UNSW Data Science Hub, University of New South Wales, Sydney, NSW 2031, Australia
| | - Kieran F. Scott
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
| | - Tara L. Roberts
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
- South Western Sydney Clinical School, UNSW, Sydney, NSW 2031, Australia
| | - Therese M. Becker
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
- South Western Sydney Clinical School, UNSW, Sydney, NSW 2031, Australia
- Centre for Circulating Tumor Cell Diagnosis and Research, Ingham Institute for Applied Medical Research, Liverpool, NSW 2170, Australia
| | - Paul de Souza
- Department of Medical Oncology, Ingham Institute of Applied Medical Research, Liverpool, NSW 2170, Australia; (Y.M.); (S.H.); (K.J.S.); (K.F.S.); (T.L.R.); (T.M.B.); (P.d.S.)
- School of Medicine, Western Sydney University, Campbelltown, NSW 2560, Australia
- South Western Sydney Clinical School, UNSW, Sydney, NSW 2031, Australia
| |
Collapse
|
26
|
Challenges in promoter methylation analysis in the new era of translational oncology: a focus on liquid biopsy. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166390. [PMID: 35296416 DOI: 10.1016/j.bbadis.2022.166390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/01/2022] [Accepted: 03/08/2022] [Indexed: 12/20/2022]
Abstract
Toward the discovery of novel reliable biomarkers, epigenetic alterations have been repeatedly proposed for the diagnosis and the development of therapeutic strategies against cancer. Indeed, for promoter methylation to actively become a tumor marker for clinical use, it must be combined with a highly informative technology evaluated in an appropriate biospecimen. Methodological standardization related to epigenetic research is, in fact, one of the most challenging tasks. Moreover, tissue-based biopsy is being complemented and, in some cases, replaced by liquid biopsy. This review will highlight the advancements made for both pre-analytical and analytical implementation for the prospective use of methylation biomarkers in clinical settings, with particular emphasis on liquid biopsy.
Collapse
|
27
|
Circulating tumour cells in the -omics era: how far are we from achieving the 'singularity'? Br J Cancer 2022; 127:173-184. [PMID: 35273384 PMCID: PMC9296521 DOI: 10.1038/s41416-022-01768-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 01/27/2022] [Accepted: 02/17/2022] [Indexed: 12/22/2022] Open
Abstract
Over the past decade, cancer diagnosis has expanded to include liquid biopsies in addition to tissue biopsies. Liquid biopsies can result in earlier and more accurate diagnosis and more effective monitoring of disease progression than tissue biopsies as samples can be collected frequently. Because of these advantages, liquid biopsies are now used extensively in clinical care. Liquid biopsy samples are analysed for circulating tumour cells (CTCs), cell-free DNA, RNA, proteins and exosomes. CTCs originate from the tumour, play crucial roles in metastasis and carry information on tumour heterogeneity. Multiple single-cell omics approaches allow the characterisation of the molecular makeup of CTCs. It has become evident that CTCs are robust biomarkers for predicting therapy response, clinical development of metastasis and disease progression. This review describes CTC biology, molecular heterogeneity within CTCs and the involvement of EMT in CTC dynamics. In addition, we describe the single-cell multi-omics technologies that have provided insights into the molecular features within therapy-resistant and metastasis-prone CTC populations. Functional studies coupled with integrated multi-omics analyses have the potential to identify therapies that can intervene the functions of CTCs.
Collapse
|
28
|
Hirahata T, ul Quraish R, Quraish AU, ul Quraish S, Naz M, Razzaq MA. Liquid Biopsy: A Distinctive Approach to the Diagnosis and Prognosis of Cancer. Cancer Inform 2022; 21:11769351221076062. [PMID: 35153470 PMCID: PMC8832574 DOI: 10.1177/11769351221076062] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/07/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer is a leading cause of morbidity and mortality worldwide. Over the past decades, the concept of precision cancer medicine has emerged as a novel approach in the field of oncology that aims to tailor the most effective treatment options to each individual cancer patient based on the genetic profile of the tumor of each individual patient. Recently, tissue biopsy has become an essential part of cancer care and is widely used to characterize the tumor. However, tissue biopsy techniques face different challenges due to their invasiveness, cost, time, and adversity in potential sampling due to tissue heterogeneity. To overcome these issues, a non-invasive approach has developed, which is known as liquid biopsy. It is a simple, fast, and worthwhile technique based on the analysis of circulating tumor DNA (which is a fraction of cfDNA), circulating tumor cells (CTCs), and other tumor-derived material in blood plasma. This review provides an overview of the concept of liquid biopsy and briefly discusses the role of ctDNA and CTC analysis as tools for early diagnosis and prognosis of cancer. In this review, we also speculate on the advantages of liquid biopsy as opposed to tissue biopsy and postulate that liquid biopsy may be a comprehensive approach to overcome the current limitations associated with costly, invasive, and time-consuming tissue biopsy.
Collapse
Affiliation(s)
| | | | | | | | - Munazzah Naz
- Hirahata Gene Therapy Laboratory, HIC Clinic, Tokyo, Japan
| | | |
Collapse
|
29
|
Sharma M, Verma RK, Kumar S, Kumar V. Computational challenges in detection of cancer using cell-free DNA methylation. Comput Struct Biotechnol J 2021; 20:26-39. [PMID: 34976309 PMCID: PMC8669313 DOI: 10.1016/j.csbj.2021.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free DNA(cfDNA) methylation profiling is considered promising and potentially reliable for liquid biopsy to study progress of diseases and develop reliable and consistent diagnostic and prognostic biomarkers. There are several different mechanisms responsible for the release of cfDNA in blood plasma, and henceforth it can provide information regarding dynamic changes in the human body. Due to the fragmented nature, low concentration of cfDNA, and high background noise, there are several challenges in its analysis for regular use in diagnosis of cancer. Such challenges in the analysis of the methylation profile of cfDNA are further aggravated due to heterogeneity, biomarker sensitivity, platform biases, and batch effects. This review delineates the origin of cfDNA methylation, its profiling, and associated computational problems in analysis for diagnosis. Here we also contemplate upon the multi-marker approach to handle the scenario of cancer heterogeneity and explore the utility of markers for 5hmC based cfDNA methylation pattern. Further, we provide a critical overview of deconvolution and machine learning methods for cfDNA methylation analysis. Our review of current methods reveals the potential for further improvement in analysis strategies for detecting early cancer using cfDNA methylation.
Collapse
Key Words
- Cancer heterogeneity
- Cell free DNA
- Computation
- DMP, Differentially methylated base position
- DMR, Differentially methylated regions
- Diagnosis
- HELP-seq, HpaII-tiny fragment Enrichment by Ligation-mediated PCR sequencing
- MBD-seq, Methyl-CpG Binding Domain Protein Capture Sequencing
- MCTA-seq, Methylated CpG tandems amplification and sequencing
- MSCC, Methylation Sensitive Cut Counting
- MSRE, methylation sensitive restriction enzymes
- MeDIP-seq, Methylated DNA Immunoprecipitation Sequencing
- RRBS, Reduced-Representation Bisulfite Sequencing
- WGBS, Whole Genome Bisulfite Sequencing
- cfDNA, cell free DNA
- ctDNA, circulating tumor DNA
- dPCR, digital polymerase chain reaction
- ddMCP, droplet digital methylation-specific PCR
- ddPCR, droplet digital polymerase chain reaction
- scCGI, methylated CGIs at single cell level
Collapse
Affiliation(s)
- Madhu Sharma
- Department for Computational Biology, Indraprastha Institute of Information Technology, Delhi 110020, India
| | - Rohit Kumar Verma
- Department for Computational Biology, Indraprastha Institute of Information Technology, Delhi 110020, India
| | - Sunil Kumar
- Department of Surgical oncology, All India Institute of Medical sciences, New Delhi 110029, India
| | - Vibhor Kumar
- Department for Computational Biology, Indraprastha Institute of Information Technology, Delhi 110020, India
| |
Collapse
|
30
|
Šutić M, Vukić A, Baranašić J, Försti A, Džubur F, Samaržija M, Jakopović M, Brčić L, Knežević J. Diagnostic, Predictive, and Prognostic Biomarkers in Non-Small Cell Lung Cancer (NSCLC) Management. J Pers Med 2021; 11:1102. [PMID: 34834454 PMCID: PMC8624402 DOI: 10.3390/jpm11111102] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/21/2021] [Accepted: 10/25/2021] [Indexed: 12/25/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Despite growing efforts for its early detection by screening populations at risk, the majority of lung cancer patients are still diagnosed in an advanced stage. The management of lung cancer has dramatically improved in the last decade and is no longer based on the "one-fits-all" paradigm or the general histological classification of non-small cell versus small cell lung cancer. Emerging options of targeted therapies and immunotherapies have shifted the management of lung cancer to a more personalized treatment approach, significantly influencing the clinical course and outcome of the disease. Molecular biomarkers have emerged as valuable tools in the prognosis and prediction of therapy response. In this review, we discuss the relevant biomarkers used in the clinical management of lung tumors, from diagnosis to prognosis. We also discuss promising new biomarkers, focusing on non-small cell lung cancer as the most abundant type of lung cancer.
Collapse
Affiliation(s)
- Maja Šutić
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.Š.); (A.V.); (J.B.)
| | - Ana Vukić
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.Š.); (A.V.); (J.B.)
| | - Jurica Baranašić
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.Š.); (A.V.); (J.B.)
| | - Asta Försti
- Hopp Children’s Cancer Center (KiTZ), 69120 Heidelberg, Germany;
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Feđa Džubur
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (F.D.); (M.S.); (M.J.)
- Clinical Department for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Miroslav Samaržija
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (F.D.); (M.S.); (M.J.)
- Clinical Department for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Marko Jakopović
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany; (F.D.); (M.S.); (M.J.)
- Clinical Department for Respiratory Diseases Jordanovac, University Hospital Centre Zagreb, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
| | - Luka Brčić
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8010 Graz, Austria;
| | - Jelena Knežević
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.Š.); (A.V.); (J.B.)
- Faculties for Dental Medicine and Health, University of Osijek, 31000 Osijek, Croatia
| |
Collapse
|
31
|
Kerachian MA, Azghandi M, Mozaffari-Jovin S, Thierry AR. Guidelines for pre-analytical conditions for assessing the methylation of circulating cell-free DNA. Clin Epigenetics 2021; 13:193. [PMID: 34663458 PMCID: PMC8525023 DOI: 10.1186/s13148-021-01182-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/04/2021] [Indexed: 02/06/2023] Open
Abstract
Methylation analysis of circulating cell-free DNA (cirDNA), as a liquid biopsy, has a significant potential to advance the detection, prognosis, and treatment of cancer, as well as many genetic disorders. The role of epigenetics in disease development has been reported in several hereditary disorders, and epigenetic modifications are regarded as one of the earliest and most significant genomic aberrations that arise during carcinogenesis. Liquid biopsy can be employed for the detection of these epigenetic biomarkers. It consists of isolation (pre-analytical) and detection (analytical) phases. The choice of pre-analytical variables comprising cirDNA extraction and bisulfite conversion methods can affect the identification of cirDNA methylation. Indeed, different techniques give a different return of cirDNA, which confirms the importance of pre-analytical procedures in clinical diagnostics. Although novel techniques have been developed for the simplification of methylation analysis, the process remains complex, as the steps of DNA extraction, bisulfite treatment, and methylation detection are each carried out separately. Recent studies have noted the absence of any standard method for the pre-analytical processing of methylated cirDNA. We have therefore conducted a comprehensive and systematic review of the important pre-analytical and analytical variables and the patient-related factors which form the basis of our guidelines for analyzing methylated cirDNA in liquid biopsy.
Collapse
Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Sina Mozaffari-Jovin
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alain R Thierry
- IRCM, Institute of Research in Oncology of Montpellier, Montpellier, France.
- INSERM, U1194, Montpellier, France.
- University of Montpellier, Montpellier, France.
- ICM, Regional Institute of Cancer of Montpellier, Montpellier, France.
| |
Collapse
|
32
|
Jung Y, Son M, Nam YR, Choi J, Heath JR, Yang S. Microfluidic Single-Cell Proteomics Assay Chip: Lung Cancer Cell Line Case Study. MICROMACHINES 2021; 12:mi12101147. [PMID: 34683198 PMCID: PMC8541572 DOI: 10.3390/mi12101147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/16/2021] [Accepted: 09/20/2021] [Indexed: 12/22/2022]
Abstract
Cancer is a dynamic disease involving constant changes. With these changes, cancer cells become heterogeneous, resulting in varying sensitivity to chemotherapy. The heterogeneity of cancer cells plays a key role in chemotherapy resistance and cancer recurrence. Therefore, for effective treatment, cancer cells need to be analyzed at the single-cell level by monitoring various proteins and investigating their heterogeneity. We propose a microfluidic chip for a single-cell proteomics assay that is capable of analyzing complex cellular signaling systems to reveal the heterogeneity of cancer cells. The single-cell assay chip comprises (i) microchambers (n = 1376) for manipulating single cancer cells, (ii) micropumps for rapid single-cell lysis, and (iii) barcode immunosensors for detecting nine different secretory and intracellular proteins to reveal the correlation among cancer-related proteins. Using this chip, the single-cell proteomics of a lung cancer cell line, which may be easily masked in bulk analysis, were evaluated. By comparing changes in the level of protein secretion and heterogeneity in response to combinations of four anti-cancer drugs, this study suggests a new method for selecting the best combination of anti-cancer drugs. Subsequent preclinical and clinical trials should enable this platform to become applicable for patient-customized therapies.
Collapse
Affiliation(s)
- Yugyung Jung
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea; (Y.J.); (M.S.); (Y.R.N.)
| | - Minkook Son
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea; (Y.J.); (M.S.); (Y.R.N.)
| | - Yu Ri Nam
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea; (Y.J.); (M.S.); (Y.R.N.)
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea
| | - Jongchan Choi
- School of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea;
- Institute for Systems Biology, Seattle, WA 98109, USA;
| | - James R. Heath
- Institute for Systems Biology, Seattle, WA 98109, USA;
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Sung Yang
- Department of Biomedical Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea; (Y.J.); (M.S.); (Y.R.N.)
- School of Mechanical Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea;
- Correspondence:
| |
Collapse
|
33
|
Surucu O, Öztürk E, Kuralay F. Nucleic Acid Integrated Technologies for Electrochemical Point‐of‐Care Diagnostics: A Comprehensive Review. ELECTROANAL 2021. [DOI: 10.1002/elan.202100309] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Ozge Surucu
- Department of Chemistry Faculty of Science Ege University 35040 Izmir Turkey
| | - Elif Öztürk
- Department of Chemistry Faculty of Science Hacettepe University 06800 Ankara Turkey
| | - Filiz Kuralay
- Department of Chemistry Faculty of Science Hacettepe University 06800 Ankara Turkey
| |
Collapse
|
34
|
Guarini C, Grassi T, Pezzicoli G, Porta C. Beyond RAS and BRAF: HER2, a New Actionable Oncotarget in Advanced Colorectal Cancer. Int J Mol Sci 2021; 22:6813. [PMID: 34202896 PMCID: PMC8268006 DOI: 10.3390/ijms22136813] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/31/2022] Open
Abstract
The human epidermal growth factor receptor 2 (HER2) is a well-established oncogenic driver and a successful therapeutic target in several malignancies, such as breast and gastric cancers. HER2 alterations, including amplification and somatic mutations, have also been detected in a small but not negligible subset of patients affected by advanced colorectal cancer (aCRC). However, to date, there are no available oncotargets in this malignancy beyond RAS and BRAF that are available. Here we present an overview on the present predictive and prognostic role of HER2 expression in aCRC, as well as on its consequent potential therapeutic implications from preclinical investigations towards ongoing trials testing anti-HER2 agents in aCRC. While HER2's role as a molecular predictive biomarker for anti-EGFR therapies in CRC is recognized, HER2 prognostic value remains controversial. Moreover, thanks to the impressive and growing body of clinical evidence, HER2 is strongly emerging as a new potential actionable oncotarget in aCRC. In conclusion, in the foreseeable future, HER2-targeted therapeutic strategies may integrate the algorithm of aCRC treatment towards an increasingly tailored therapeutic approach to this disease.
Collapse
Affiliation(s)
- Chiara Guarini
- Post-Graduate School of Specialization in Medical Oncology, University of Bari ‘Aldo Moro’, 70124 Bari, Italy;
- Division of Medical Oncology, A.O.U. Consorziale Policlinico di Bari, 70124 Bari, Italy; (T.G.); (C.P.)
| | - Teresa Grassi
- Division of Medical Oncology, A.O.U. Consorziale Policlinico di Bari, 70124 Bari, Italy; (T.G.); (C.P.)
| | - Gaetano Pezzicoli
- Post-Graduate School of Specialization in Medical Oncology, University of Bari ‘Aldo Moro’, 70124 Bari, Italy;
- Division of Medical Oncology, A.O.U. Consorziale Policlinico di Bari, 70124 Bari, Italy; (T.G.); (C.P.)
| | - Camillo Porta
- Division of Medical Oncology, A.O.U. Consorziale Policlinico di Bari, 70124 Bari, Italy; (T.G.); (C.P.)
- Chair of Oncology, Department of Biomedical Sciences and Human Oncology, University of Bari ‘A. Moro’, 70124 Bari, Italy
| |
Collapse
|
35
|
Xu C, He XY, Ren XH, Cheng SX. Direct detection of intracellular miRNA in living circulating tumor cells by tumor targeting nanoprobe in peripheral blood. Biosens Bioelectron 2021; 190:113401. [PMID: 34119837 DOI: 10.1016/j.bios.2021.113401] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/24/2021] [Accepted: 06/01/2021] [Indexed: 02/07/2023]
Abstract
Molecular analysis of circulating tumor cells (CTCs) is of critical significance for the non-invasive early detection of tumors. However, in situ detection of intracellular nucleic acids of CTCs in whole blood still remains challenge. By using a highly efficient tumor targeting nanoprobe, we realize in situ detection of microRNA-21 (miR-21) of living CTCs in unprocessed whole blood. In the nanoprobe, a catalytic hairpin assembly (CHA) system is complexed with protamine sulfate (PS), and then decorated by SYL3C conjugated hyaluronic acid (SHA) and hyaluronic acid (HA). The CHA system can be specifically delivered into living CTCs in whole blood, followed by hybridization between the CHA system and intracellular miR-21 in CTCs to induce strong fluorescence emission. After isolation of CTCs by membrane filtration, CTCs of cancer patients can be directly visualized by a fluorescence microscope for miR-21 detection at a single-cell level. Our study provides an efficient strategy to realize in situ genomic analysis of living CTCs in whole blood.
Collapse
Affiliation(s)
- Chang Xu
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
| | - Xiao-Yan He
- School of Life Sciences, Anhui Medical University, Hefei, 230032, PR China
| | - Xiao-He Ren
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
| | - Si-Xue Cheng
- Key Laboratory of Biomedical Polymers of Ministry of Education, Department of Chemistry, Wuhan University, Wuhan, 430072, PR China.
| |
Collapse
|
36
|
Williams PM, Forbes T, P. Lund S, Cole KD, He HJ, Karlovich C, Paweletz CP, Stetson D, Yee LM, Connors DE, Keating SM, Destenaves B, Cleveland MH, Lau CJ, Barrett JC, Kelloff GJ, McCormack RT. Validation of ctDNA Quality Control Materials Through a Precompetitive Collaboration of the Foundation for the National Institutes of Health. JCO Precis Oncol 2021; 5:PO.20.00528. [PMID: 34250423 PMCID: PMC8232894 DOI: 10.1200/po.20.00528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 03/05/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022] Open
Abstract
We report the results from a Foundation for the National Institutes of Health Biomarkers Consortium project to address the absence of well-validated quality control materials (QCMs) for circulating tumor DNA (ctDNA) testing. This absence is considered a cause of variance and inconsistencies in translating ctDNA results into clinical actions. METHODS In this phase I study, QCMs with 14 clinically relevant mutations representing single nucleotide variants, insertions or deletions (indels), translocations, and copy number variants were sourced from three commercial manufacturers with variant allele frequencies (VAFs) of 5%, 2.5%, 1%, 0.1%, and 0%. Four laboratories tested samples in quadruplicate using two allele-specific droplet digital polymerase chain reaction and three (amplicon and hybrid capture) next-generation sequencing (NGS) panels. RESULTS The two droplet digital polymerase chain reaction assays reported VAF values very close to the manufacturers' claimed concentrations for all QCMs. NGS assays reported most single nucleotide variants and indels, but not translocations, close to the expected VAF values. Notably, two NGS assays reported lower VAF than expected for all translocations in all QCM mixtures, possibly related to technical challenges detecting these variants. The ability to call ERBB2 copy number amplifications varied across assays. All three QCMs provided valuable insight into assay precision. Each assay across all variant types demonstrated dropouts at 0.1%, suggesting that the QCM can serve for testing of an assay's limit of detection with confidence claims for specific variants. CONCLUSION These results support the utility of the QCM in testing ctDNA assay analytical performance. However, unique designs and manufacturing methods for the QCM, and variations in a laboratory's testing configuration, may require testing of multiple QCMs to find the best reagents for accurate result interpretation.
Collapse
Affiliation(s)
- P. Mickey Williams
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD
| | - Thomas Forbes
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD
| | - Steven P. Lund
- National Institute of Standards and Technology, Gaithersburg, MD
| | - Kenneth D. Cole
- National Institute of Standards and Technology, Gaithersburg, MD
| | - Hua-Jun He
- National Institute of Standards and Technology, Gaithersburg, MD
| | - Chris Karlovich
- Molecular Characterization Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD
| | - Cloud P. Paweletz
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - Daniel Stetson
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | - Laura M. Yee
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Dana E. Connors
- Foundation for the National Institutes of Health, Bethesda, MD
| | | | | | | | - Christie J. Lau
- Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - J. Carl Barrett
- Translational Medicine, Oncology R&D, AstraZeneca, Waltham, MA
| | | | | |
Collapse
|
37
|
Liang W, Chen Z, Li C, Liu J, Tao J, Liu X, Zhao D, Yin W, Chen H, Cheng C, Yu F, Zhang C, Liu L, Tian H, Cai K, Liu X, Wang Z, Xu N, Dong Q, Chen L, Yang Y, Zhi X, Li H, Tu X, Cai X, Jiang Z, Ji H, Mo L, Wang J, Fan JB, He J. Accurate diagnosis of pulmonary nodules using a noninvasive DNA methylation test. J Clin Invest 2021; 131:145973. [PMID: 33793424 PMCID: PMC8121527 DOI: 10.1172/jci145973] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/18/2021] [Indexed: 02/05/2023] Open
Abstract
BACKGROUNDCurrent clinical management of patients with pulmonary nodules involves either repeated low-dose CT (LDCT)/CT scans or invasive procedures, yet causes significant patient misclassification. An accurate noninvasive test is needed to identify malignant nodules and reduce unnecessary invasive tests.METHODWe developed a diagnostic model based on targeted DNA methylation sequencing of 389 pulmonary nodule patients' plasma samples and then validation in 140 plasma samples independently. We tested the model in different stages and subtypes of pulmonary nodules.RESULTSA 100-feature model was developed and validated for pulmonary nodule diagnosis; the model achieved a receiver operating characteristic curve-AUC (ROC-AUC) of 0.843 on 140 independent validation samples, with an accuracy of 0.800. The performance was well maintained in (a) a 6 to 20 mm size subgroup (n = 100), with a sensitivity of 1.000 and adjusted negative predictive value (NPV) of 1.000 at 10% prevalence; (b) stage I malignancy (n = 90), with a sensitivity of 0.971; (c) different nodule types: solid nodules (n = 78) with a sensitivity of 1.000 and adjusted NPV of 1.000, part-solid nodules (n = 75) with a sensitivity of 0.947 and adjusted NPV of 0.983, and ground-glass nodules (n = 67) with a sensitivity of 0.964 and adjusted NPV of 0.989 at 10% prevalence. This methylation test, called PulmoSeek, outperformed PET-CT and 2 clinical prediction models (Mayo Clinic and Veterans Affairs) in discriminating malignant pulmonary nodules from benign ones.CONCLUSIONThis study suggests that the blood-based DNA methylation model may provide a better test for classifying pulmonary nodules, which could help facilitate the accurate diagnosis of early stage lung cancer from pulmonary nodule patients and guide clinical decisions.FUNDINGThe National Key Research and Development Program of China; Science and Technology Planning Project of Guangdong Province; The National Natural Science Foundation of China National.
Collapse
Affiliation(s)
- Wenhua Liang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Zhiwei Chen
- AnchorDx Medical Co., Guangzhou, China
- AnchorDx Inc., Fremont, California, USA
| | - Caichen Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Jun Liu
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | | | - Xin Liu
- AnchorDx Inc., Fremont, California, USA
| | | | - Weiqiang Yin
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Hanzhang Chen
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Chao Cheng
- Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Chunfang Zhang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Luxu Liu
- Department of Thoracic Surgery, West China Hospital of Sichuan University, Chengdu, China
| | - Hui Tian
- Department of Thoracic Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Kaican Cai
- Department of Thoracic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Xiang Liu
- Department of Thoracic Surgery, The Second Hospital, University of South China, Hengyang, China
| | - Zheng Wang
- Department of Thoracic Surgery, Shenzhen People’s Hospital, Shenzhen, China
| | - Ning Xu
- Department of Thoracic Surgery, Anhui Chest Hospital, Hefei, China
| | - Qing Dong
- Department of Thoracic Surgery, Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Liang Chen
- Department of Thoracic Surgery, Jiangsu Province Hospital, Nanjing, China
| | - Yue Yang
- Department of Thoracic Surgery, Beijing Cancer Hospital, Beijing, China
| | - Xiuyi Zhi
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| | - Hui Li
- AnchorDx Medical Co., Guangzhou, China
| | | | - Xiangrui Cai
- College of Computer Science, Nankai University, Tianjin, China
| | | | - Hua Ji
- College of Computer Science, Nankai University, Tianjin, China
- Laboratory for Foundations of Computer Science, School of Informatics, University of Edinburgh, United Kingdom
| | - Lili Mo
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Jiaxuan Wang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, China
| | - Jian-Bing Fan
- AnchorDx Medical Co., Guangzhou, China
- Department of Pathology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Jianxing He
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, China National Center for Respiratory Medicine, China State Key Laboratory of Respiratory Disease & National Clinical Research Center for Respiratory Disease, Guangzhou, China
- Department of Thoracic Surgery, Nanfang Hospital of Southern Medical University, Guangzhou, China
| |
Collapse
|
38
|
Laurenzana I, Trino S, Lamorte D, Girasole M, Dinarelli S, De Stradis A, Grieco V, Maietti M, Traficante A, Statuto T, Villani O, Musto P, Sgambato A, De Luca L, Caivano A. Analysis of Amount, Size, Protein Phenotype and Molecular Content of Circulating Extracellular Vesicles Identifies New Biomarkers in Multiple Myeloma. Int J Nanomedicine 2021; 16:3141-3160. [PMID: 33994784 PMCID: PMC8114829 DOI: 10.2147/ijn.s303391] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/11/2021] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION Extracellular vesicles (EVs) are naturally secreted cellular lipid bilayer particles, which carry a selected molecular content. Owing to their systemic availability and their role in tumor pathogenesis, circulating EVs (cEVs) can be a valuable source of new biomarkers useful for tumor diagnosis, prognostication and monitoring. However, a precise approach for isolation and characterization of cEVs as tumor biomarkers, exportable in a clinical setting, has not been conclusively established. METHODS We developed a novel and laboratory-made procedure based on a bench centrifuge step which allows the isolation of serum cEVs suitable for subsequent characterization of their size, amount and phenotype by nanoparticle tracking analysis, microscopy and flow cytometry, and for nucleic acid assessment by digital PCR. RESULTS Applied to blood from healthy subjects (HSs) and tumor patients, our approach permitted from a small volume of serum (i) the isolation of a great amount of EVs enriched in small vesicles free from protein contaminants; (ii) a suitable and specific cell origin identification of EVs, and (iii) nucleic acid content assessment. In clonal plasma cell malignancy, like multiple myeloma (MM), our approach allowed us to identify specific MM EVs, and to characterize their size, concentration and microRNA content allowing significant discrimination between MM and HSs. Finally, EV associated biomarkers correlated with MM clinical parameters. CONCLUSION Overall, our cEV based procedure can play an important role in malignancy biomarker discovery and then in real-time tumor monitoring using minimal invasive samples. From a practical point of view, it is smart (small sample volume), rapid (two hours), easy (no specific expertise required) and requirements are widely available in clinical laboratories.
Collapse
Affiliation(s)
- Ilaria Laurenzana
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Stefania Trino
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Daniela Lamorte
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Marco Girasole
- Institute for the Study of the Structure of Matter, National Research Council (CNR), Rome, Italy
| | - Simone Dinarelli
- Institute for the Study of the Structure of Matter, National Research Council (CNR), Rome, Italy
| | - Angelo De Stradis
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Vitina Grieco
- Laboratory of Clinical Research and Advanced Diagnostics, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Maddalena Maietti
- Unit of Clinical Pathology, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Antonio Traficante
- Unit of Clinical Pathology, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Teodora Statuto
- Laboratory of Clinical Research and Advanced Diagnostics, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Oreste Villani
- Hematology and Stem Cell Transplantation Unit, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Pellegrino Musto
- Hematology and Stem Cell Transplantation Unit, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Alessandro Sgambato
- Scientific Direction, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Luciana De Luca
- Laboratory of Clinical Research and Advanced Diagnostics, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Antonella Caivano
- Laboratory of Clinical Research and Advanced Diagnostics, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| |
Collapse
|
39
|
Augustus E, Zwaenepoel K, Siozopoulou V, Raskin J, Jordaens S, Baggerman G, Sorber L, Roeyen G, Peeters M, Pauwels P. Prognostic and Predictive Biomarkers in Non-Small Cell Lung Cancer Patients on Immunotherapy-The Role of Liquid Biopsy in Unraveling the Puzzle. Cancers (Basel) 2021; 13:1675. [PMID: 33918147 PMCID: PMC8036384 DOI: 10.3390/cancers13071675] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 03/29/2021] [Accepted: 03/30/2021] [Indexed: 12/14/2022] Open
Abstract
In the last decade, immunotherapy has been one of the most important advances in the non-small cell lung cancer (NSCLC) treatment landscape. Nevertheless, only a subset of NSCLC patients benefits from it. Currently, the only Food and Drug Administration (FDA) approved diagnostic test for first-line immunotherapy in metastatic NSCLC patients uses tissue biopsies to determine the programmed death ligand 1 (PD-L1) status. However, obtaining tumor tissue is not always feasible and puts the patient at risk. Liquid biopsy, which refers to the tumor-derived material present in body fluids, offers an alternative approach. This less invasive technique gives real-time information on the tumor characteristics. This review addresses different promising liquid biopsy based biomarkers in NSCLC patients that enable the selection of patients who benefit from immunotherapy and the monitoring of patients during this therapy. The challenges and the opportunities of blood-based biomarkers such as cell-free DNA (cfDNA), circulating tumor cells (CTCs), exosomes, epigenetic signatures, microRNAs (miRNAs) and the T cell repertoire will be addressed. This review also focuses on the less-studied feces-based and breath-based biomarkers.
Collapse
Affiliation(s)
- Elien Augustus
- Center for Oncological Research Antwerp (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp (UAntwerp), 2610 Wilrijk, Belgium; (K.Z.); (V.S.); (S.J.); (L.S.); (M.P.); (P.P.)
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | - Karen Zwaenepoel
- Center for Oncological Research Antwerp (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp (UAntwerp), 2610 Wilrijk, Belgium; (K.Z.); (V.S.); (S.J.); (L.S.); (M.P.); (P.P.)
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | - Vasiliki Siozopoulou
- Center for Oncological Research Antwerp (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp (UAntwerp), 2610 Wilrijk, Belgium; (K.Z.); (V.S.); (S.J.); (L.S.); (M.P.); (P.P.)
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | - Jo Raskin
- Department of Pulmonology and Thoracic Oncology, Antwerp University Hospital (UZA), 2650 Edegem, Belgium;
| | - Stephanie Jordaens
- Center for Oncological Research Antwerp (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp (UAntwerp), 2610 Wilrijk, Belgium; (K.Z.); (V.S.); (S.J.); (L.S.); (M.P.); (P.P.)
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | - Geert Baggerman
- Centre for Proteomics, University of Antwerp (UAntwerp), 2020 Antwerpen, Belgium;
- Health Unit, Vlaamse Instelling voor Technologisch Onderzoek (VITO), 2400 Mol, Belgium
| | - Laure Sorber
- Center for Oncological Research Antwerp (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp (UAntwerp), 2610 Wilrijk, Belgium; (K.Z.); (V.S.); (S.J.); (L.S.); (M.P.); (P.P.)
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | - Geert Roeyen
- Department of Hepato-Pancreato-Biliary, Endocrine and Transplantation Surgery, Antwerp University Hospital (UZA), 2650 Edegem, Belgium;
| | - Marc Peeters
- Center for Oncological Research Antwerp (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp (UAntwerp), 2610 Wilrijk, Belgium; (K.Z.); (V.S.); (S.J.); (L.S.); (M.P.); (P.P.)
- Department of Oncology, Multidisciplinary Oncological Center Antwerp, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | - Patrick Pauwels
- Center for Oncological Research Antwerp (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp (UAntwerp), 2610 Wilrijk, Belgium; (K.Z.); (V.S.); (S.J.); (L.S.); (M.P.); (P.P.)
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| |
Collapse
|
40
|
Pisapia P, Costa JL, Pepe F, Russo G, Gragnano G, Russo A, Iaccarino A, de Miguel-Perez D, Serrano MJ, Denninghoff V, Quagliata L, Rolfo C, Malapelle U. Next generation sequencing for liquid biopsy based testing in non-small cell lung cancer in 2021. Crit Rev Oncol Hematol 2021; 161:103311. [PMID: 33781866 DOI: 10.1016/j.critrevonc.2021.103311] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/15/2022] Open
Abstract
Lung cancer is the leading cause of cancer death worldwide, with non-small cell lung cancer (NSCLC) representing its most commonly diagnosed sub-type. Despite the significant improvements in lung cancer biomarkers knowledge, accompanied by substantial technological advances in molecular tumor profiling, a considerable fraction (up to 30 %) of advanced NSCLC patient presents with major testing challenges or tissue unavailability for molecular analysis. In this context, liquid biopsy is on the rise, currently gaining considerable interest within the molecular pathology and oncology community. Molecular profiling of liquid biopsy specimens using next generation molecular biology methodologies is a rapidly evolving field with promising applications not exclusively limited to advanced stages but also more recently expanding to early stages cancer patients. Here, we offer an overview of some of the most consolidated and emerging applications of next generation sequencing technologies for liquid biopsy testing in NSCLC.
Collapse
Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - José Luis Costa
- Medical Affairs Clinical NGS and Oncology Division Life Sciences Solutions, Thermo Fisher Scientific, Zug, Switzerland
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Gragnano
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | - Antonino Iaccarino
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Diego de Miguel-Perez
- Liquid Biopsy and Metastasis Research Group, GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government PTS, Granada, Spain; Thoracic Medical Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Maria Josè Serrano
- Liquid Biopsy and Metastasis Research Group, GENYO, Centre for Genomics and Oncological Research: Pfizer, University of Granada, Andalusian Regional Government PTS, Granada, Spain
| | - Valeria Denninghoff
- University of Buenos Aires - National Council for Scientific and Technical Research (CONICET), Buenos Aires, Argentina
| | - Luca Quagliata
- Medical Affairs Clinical NGS and Oncology Division Life Sciences Solutions, Thermo Fisher Scientific, Zug, Switzerland
| | - Christian Rolfo
- Thoracic Medical Oncology, Marlene and Stewart Greenebaum Cancer Center, University of Maryland, Baltimore, MD, USA
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy.
| |
Collapse
|
41
|
Tieng FYF, Abu N, Lee LH, Ab Mutalib NS. Microsatellite Instability in Colorectal Cancer Liquid Biopsy-Current Updates on Its Potential in Non-Invasive Detection, Prognosis and as a Predictive Marker. Diagnostics (Basel) 2021; 11:544. [PMID: 33803882 PMCID: PMC8003257 DOI: 10.3390/diagnostics11030544] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 12/24/2022] Open
Abstract
Colorectal cancer (CRC) is the third most commonly-diagnosed cancer in the world and ranked second for cancer-related mortality in humans. Microsatellite instability (MSI) is an indicator for Lynch syndrome (LS), an inherited cancer predisposition, and a prognostic marker which predicts the response to immunotherapy. A recent trend in immunotherapy has transformed cancer treatment to provide medical alternatives that have not existed before. It is believed that MSI-high (MSI-H) CRC patients would benefit from immunotherapy due to their increased immune infiltration and higher neo-antigenic loads. MSI testing such as immunohistochemistry (IHC) and PCR MSI assay has historically been a tissue-based procedure that involves the testing of adequate tissue with a high concentration of cancer cells, in addition to the requirement for paired normal tissues. The invasive nature and specific prerequisite of such tests might hinder its application when surgery is not an option or when the tissues are insufficient. The application of next-generation sequencing, which is highly sensitive, in combination with liquid biopsy, therefore, presents an interesting possibility worth exploring. This review aimed to discuss the current body of evidence supporting the potential of liquid biopsy as a tool for MSI testing in CRC.
Collapse
Affiliation(s)
- Francis Yew Fu Tieng
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.)
| | - Nadiah Abu
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.)
| | - Learn-Han Lee
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor 47500, Malaysia
| | - Nurul-Syakima Ab Mutalib
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Kuala Lumpur 56000, Malaysia; (F.Y.F.T.); (N.A.)
- Novel Bacteria and Drug Discovery Research Group, Microbiome and Bioresource Research Strength, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Selangor 47500, Malaysia
- Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur 50300, Malaysia
| |
Collapse
|
42
|
Belotti Y, Lim CT. Microfluidics for Liquid Biopsies: Recent Advances, Current Challenges, and Future Directions. Anal Chem 2021; 93:4727-4738. [DOI: 10.1021/acs.analchem.1c00410] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yuri Belotti
- Institute for Health Innovation and Technology, National University of Singapore, 117599 Singapore
| | - Chwee Teck Lim
- Institute for Health Innovation and Technology, National University of Singapore, 117599 Singapore
- Department of Biomedical Engineering, National University of Singapore, 117583 Singapore
- Mechanobiology Institute, National University of Singapore, 117411 Singapore
| |
Collapse
|
43
|
Brisotto G, Guerrieri R, Colizzi F, Steffan A, Montico B, Fratta E. Long Noncoding RNAs as Innovative Urinary Diagnostic Biomarkers. Methods Mol Biol 2021; 2292:73-94. [PMID: 33651353 DOI: 10.1007/978-1-0716-1354-2_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The characterization of circulating tumor cells (CTCs) is now widely studied as a promising source of cancer-derived biomarkers because of their role in tumor formation and progression. However, CTCs analysis presents some limitations and no standardized method for CTCs isolation from urine has been defined so far. In fact, besides blood, urine represents an ideal source of noninvasive biomarkers, especially for the early detection of genitourinary tumors. Besides CTCs, long noncoding RNAs (lncRNAs) have also been proposed as potential noninvasive biomarkers, and the evaluation of the diagnostic accuracy of urinary lncRNAs has dramatically increased over the last years, with many studies being published. Therefore, this review provides an update on the clinical utility of urinary lncRNAs as novel biomarkers for the diagnosis of bladder and prostate cancers.
Collapse
Affiliation(s)
- Giulia Brisotto
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Roberto Guerrieri
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Francesca Colizzi
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Barbara Montico
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy
| | - Elisabetta Fratta
- Immunopathology and Cancer Biomarkers, Centro di Riferimento Oncologico di Aviano (CRO), IRCCS, Aviano, Italy.
| |
Collapse
|
44
|
Pinzani P, D'Argenio V, Del Re M, Pellegrini C, Cucchiara F, Salvianti F, Galbiati S. Updates on liquid biopsy: current trends and future perspectives for clinical application in solid tumors. Clin Chem Lab Med 2021; 59:1181-1200. [PMID: 33544478 DOI: 10.1515/cclm-2020-1685] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 01/20/2021] [Indexed: 01/19/2023]
Abstract
Despite advances in screening and therapeutics cancer continues to be one of the major causes of morbidity and mortality worldwide. The molecular profile of tumor is routinely assessed by surgical or bioptic samples, however, genotyping of tissue has inherent limitations: it represents a single snapshot in time and it is subjected to spatial selection bias owing to tumor heterogeneity. Liquid biopsy has emerged as a novel, non-invasive opportunity of detecting and monitoring cancer in several body fluids instead of tumor tissue. Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), RNA (mRNA and microRNA), microvesicles, including exosomes and tumor "educated platelets" were recently identified as a source of genomic information in cancer patients which could reflect all subclones present in primary and metastatic lesions allowing sequential monitoring of disease evolution. In this review, we summarize the currently available information concerning liquid biopsy in breast cancer, colon cancer, lung cancer and melanoma. These promising issues still need to be standardized and harmonized across laboratories, before fully adopting liquid biopsy approaches into clinical practice.
Collapse
Affiliation(s)
- Pamela Pinzani
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Valeria D'Argenio
- Department of Human Sciences and Quality of Life Promotion, San Raffaele Open University, Rome, Italy.,CEINGE-Biotecnologie Avanzate, Naples, Italy
| | - Marzia Del Re
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Cristina Pellegrini
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Federico Cucchiara
- Clinical Pharmacology and Pharmacogenetics Unit, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Francesca Salvianti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Silvia Galbiati
- Diabetes Research Institute, IRCCS Ospedale San Raffaele, Milan, Italy
| |
Collapse
|
45
|
Parisi A, Porzio G, Pulcini F, Cannita K, Ficorella C, Mattei V, Delle Monache S. What Is Known about Theragnostic Strategies in Colorectal Cancer. Biomedicines 2021; 9:biomedicines9020140. [PMID: 33535557 PMCID: PMC7912746 DOI: 10.3390/biomedicines9020140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
Despite the paradigmatic shift occurred in recent years for defined molecular subtypes in the metastatic setting treatment, colorectal cancer (CRC) still remains an incurable disease in most of the cases. Therefore, there is an urgent need for new tools and biomarkers for both early tumor diagnosis and to improve personalized treatment. Thus, liquid biopsy has emerged as a minimally invasive tool that is capable of detecting genomic alterations from primary or metastatic tumors, allowing the prognostic stratification of patients, the detection of the minimal residual disease after surgical or systemic treatments, the monitoring of therapeutic response, and the development of resistance, establishing an opportunity for early intervention before imaging detection or worsening of clinical symptoms. On the other hand, preclinical and clinical evidence demonstrated the role of gut microbiota dysbiosis in promoting inflammatory responses and cancer initiation. Altered gut microbiota is associated with resistance to chemo drugs and immune checkpoint inhibitors, whereas the use of microbe-targeted therapies including antibiotics, pre-probiotics, and fecal microbiota transplantation can restore response to anticancer drugs, promote immune response, and therefore support current treatment strategies in CRC. In this review, we aim to summarize preclinical and clinical evidence for the utilization of liquid biopsy and gut microbiota in CRC.
Collapse
Affiliation(s)
- Alessandro Parisi
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
- Medical Oncology Unit, St. Salvatore Hospital, 67100 L’Aquila, Italy; (G.P.); (K.C.); (C.F.)
| | - Giampiero Porzio
- Medical Oncology Unit, St. Salvatore Hospital, 67100 L’Aquila, Italy; (G.P.); (K.C.); (C.F.)
- Department of Biotechnology and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Fanny Pulcini
- Department of Biotechnology and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Katia Cannita
- Medical Oncology Unit, St. Salvatore Hospital, 67100 L’Aquila, Italy; (G.P.); (K.C.); (C.F.)
- Department of Biotechnology and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Corrado Ficorella
- Medical Oncology Unit, St. Salvatore Hospital, 67100 L’Aquila, Italy; (G.P.); (K.C.); (C.F.)
- Department of Biotechnology and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Vincenzo Mattei
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, via Angelo Maria Ricci 35A, 02100 Rieti, Italy;
| | - Simona Delle Monache
- Department of Biotechnology and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
- Correspondence: ; Tel.: +39-086-243-3569
| |
Collapse
|
46
|
Barefoot ME, Lindberg MR, Wellstein A. Decoding the Tissue of Origin of Cellular Damage from Cell-Free DNA in Liquid Biopsies. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11669-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
|
47
|
Koçana CÇ, Toprak SF, Sözer S. Extracellular genetic materials and their application in clinical practice. Cancer Genet 2020; 252-253:48-63. [PMID: 33387935 DOI: 10.1016/j.cancergen.2020.12.006] [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: 06/11/2020] [Revised: 11/12/2020] [Accepted: 12/20/2020] [Indexed: 11/20/2022]
Abstract
This study reviews the possible origins, functional roles, and diagnostic applications of 'extracellular genetic material' (EGM), a novel term introduced to cover DNA, RNA, and DNA/RNA-related molecules released from all types of cells into the extracellular region. The literature on EGMs shows them to play a dual role in diverse, fine-tuning mechanisms involved in both homeostasis and pathological events, including cancerogenesis and genometastasis. Recent developments in the next-generation technology have provided successful applications of low quantities of genomic materials into the diagnostic field, yielding high sensitivity and specificity in test results. Also, the successful application of EGMs into diagnostics has afforded promising outcomes for researchers and clinicians. This study of EGM provides a deeper understanding of the subject as an area of interest, especially cell-free DNA, aiming toward the eventual development of new therapeutic applications and diagnostic strategies.
Collapse
Affiliation(s)
- Cemal Çağıl Koçana
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selin Fulya Toprak
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selçuk Sözer
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
| |
Collapse
|
48
|
Jang JY, Kim YS, Kang KN, Kim KH, Park YJ, Kim CW. Multiple microRNAs as biomarkers for early breast cancer diagnosis. Mol Clin Oncol 2020; 14:31. [PMID: 33414912 PMCID: PMC7783718 DOI: 10.3892/mco.2020.2193] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/07/2020] [Indexed: 12/26/2022] Open
Abstract
MicroRNA (miRNA or miR) is stably present in plasma. It has been reported that miRNA could be used for detecting cancer. Circulating miRNAs are being increasingly recognized as powerful biomarkers in a number of different pathologies, including in breast cancer. The aim of the current study was to establish and validate miRNA sets that are useful for the early diagnosis of breast cancer. Specifically, the current study intended to determine whether miRNA biomarkers were tumor-specific and to statistically verify whether circulating miRNA analysis could be used for breast cancer diagnosis. In the present study, a total of nine candidate miRNA biomarkers were selected by examining reference miRNAs associated with the generation and progression of breast cancer to identify novel miRNAs that could be used to detect early breast cancer. A total of 226 plasma samples from patients with breast cancer were used. In addition, 146 plasma healthy samples were used as non-cancer controls. These samples were divided into training and validation cohorts. The training cohort was used to identify a combination of miRNA that could detect breast cancer. The validation cohort was used to validate this combination of miRNA. Total RNAs were isolated from collected samples. A total of 9 miRNAs were quantified using reverse-transcription quantitative PCR. A total of nine candidate miRNA expression levels were compared between patients with breast cancer and healthy controls. It was indicated that combinations of two or more of the nine miRNAs could detect breast cancer with higher accuracy than the use of a single biomarker. As a representative example, combinations of four miRNAs (miR-1246+miR-206+miR-24+miR-373) of the nine miRNAs had a sensitivity of 98%, a specificity of 96% and an accuracy of 97% for breast cancer detection in the validation cohort. The results of the present study suggest that multiple miRNAs could be used as potential biomarkers for early diagnosis of breast cancer. These biomarkers are expected to overcome limitations of mammography when used as an auxiliary diagnosis of mammography.
Collapse
Affiliation(s)
- Ji Young Jang
- BIOINFRA Life Science Inc., Jongno-gu, Seoul 03127, Republic of Korea
| | - Yeon Soo Kim
- DIOGENE Inc., Bundang-gu, Seongnam-Si 13486, Republic of Korea
| | - Kyung Nam Kang
- BIOINFRA Life Science Inc., Jongno-gu, Seoul 03127, Republic of Korea
| | - Kyo Hyun Kim
- DIOGENE Inc., Bundang-gu, Seongnam-Si 13486, Republic of Korea
| | - Yu Jin Park
- BIOINFRA Life Science Inc., Jongno-gu, Seoul 03127, Republic of Korea
| | - Chul Woo Kim
- BIOINFRA Life Science Inc., Jongno-gu, Seoul 03127, Republic of Korea
| |
Collapse
|
49
|
Taylor C, Chacko S, Davey M, Lacroix J, MacPherson A, Finn N, Wajnberg G, Ghosh A, Crapoulet N, Lewis SM, Ouellette RJ. Peptide-Affinity Precipitation of Extracellular Vesicles and Cell-Free DNA Improves Sequencing Performance for the Detection of Pathogenic Mutations in Lung Cancer Patient Plasma. Int J Mol Sci 2020; 21:E9083. [PMID: 33260345 PMCID: PMC7730179 DOI: 10.3390/ijms21239083] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/12/2022] Open
Abstract
Liquid biopsy is a minimally-invasive diagnostic method that may improve access to molecular profiling for non-small cell lung cancer (NSCLC) patients. Although cell-free DNA (cf-DNA) isolation from plasma is the standard liquid biopsy method for detecting DNA mutations in cancer patients, the sensitivity can be highly variable. Vn96 is a peptide with an affinity for both extracellular vesicles (EVs) and circulating cf-DNA. In this study, we evaluated whether peptide-affinity (PA) precipitation of EVs and cf-DNA from NSCLC patient plasma improves the sensitivity of single nucleotide variants (SNVs) detection and compared observed SNVs with those reported in the matched tissue biopsy. NSCLC patient plasma was subjected to either PA precipitation or cell-free methods and total nucleic acid (TNA) was extracted; SNVs were then detected by next-generation sequencing (NGS). PA led to increased recovery of DNA as well as an improvement in NGS sequencing parameters when compared to cf-TNA. Reduced concordance with tissue was observed in PA-TNA (62%) compared to cf-TNA (81%), mainly due to identification of SNVs in PA-TNA that were not observed in tissue. EGFR mutations were detected in PA-TNA with 83% sensitivity and 100% specificity. In conclusion, PA-TNA may improve the detection limits of low-abundance alleles using NGS.
Collapse
Affiliation(s)
- Catherine Taylor
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Simi Chacko
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Michelle Davey
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Jacynthe Lacroix
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Alexander MacPherson
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Nicholas Finn
- Dr Léon-Richard Oncology Center, Moncton, NB E1C 8X3, Canada;
| | - Gabriel Wajnberg
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Anirban Ghosh
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Nicolas Crapoulet
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
| | - Stephen M. Lewis
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
- Department of Chemistry & Biochemistry, Université de Moncton, Moncton, NB E1A 3E9, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
| | - Rodney J. Ouellette
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada; (C.T.); (S.C.); (M.D.); (J.L.); (A.M.); (G.W.); (A.G.); (N.C.); (S.M.L.)
- Department of Chemistry & Biochemistry, Université de Moncton, Moncton, NB E1A 3E9, Canada
| |
Collapse
|
50
|
Sharbatoghli M, Vafaei S, Aboulkheyr Es H, Asadi-Lari M, Totonchi M, Madjd Z. Prediction of the treatment response in ovarian cancer: a ctDNA approach. J Ovarian Res 2020; 13:124. [PMID: 33076944 PMCID: PMC7574472 DOI: 10.1186/s13048-020-00729-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/11/2020] [Indexed: 02/06/2023] Open
Abstract
Ovarian cancer is the eighth most commonly occurring cancer in women. Clinically, the limitation of conventional screening and monitoring approaches inhibits high throughput analysis of the tumor molecular markers toward prediction of treatment response. Recently, analysis of liquid biopsies including circulating tumor DNA (ctDNA) open new way toward cancer diagnosis and treatment in a personalized manner in various types of solid tumors. In the case of ovarian carcinoma, growing pre-clinical and clinical studies underscored promising application of ctDNA in diagnosis, prognosis, and prediction of treatment response. In this review, we accumulate and highlight recent molecular findings of ctDNA analysis and its associations with treatment response and patient outcome. Additionally, we discussed the potential application of ctDNA in the personalized treatment of ovarian carcinoma. ctDNA-monitoring usage during the ovarian cancer treatments procedures.
Collapse
Affiliation(s)
- Mina Sharbatoghli
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Somayeh Vafaei
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Mohsen Asadi-Lari
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Epidemiology, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Mehdi Totonchi
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran.
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran.
| | - Zahra Madjd
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran.
- Department of Molecular Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|