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Tavano F, Latiano A, Palmieri O, Gioffreda D, Latiano T, Gentile A, Tardio M, Latiano TP, Gentile M, Terracciano F, Perri F. Duodenal Fluid Analysis as a Rewarding Approach to Detect Low-Abundance Mutations in Biliopancreatic Cancers. Int J Mol Sci 2024; 25:8436. [PMID: 39126005 PMCID: PMC11312909 DOI: 10.3390/ijms25158436] [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: 06/20/2024] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 08/12/2024] Open
Abstract
Diagnosis of biliopancreatic cancers by the available serum tumor markers, imaging, and histopathological tissue specimen examination remains a challenge. Circulating cell-free DNA derived from matched pairs of secretin-stimulated duodenal fluid (DF) and plasma from 10 patients with biliopancreatic diseases and 8 control subjects was analyzed using AmpliSeq™ HD technology for Ion Torrent Next-Generation Sequencing to evaluate the potential of liquid biopsy with DF in biliopancreatic cancers. The median cfDNA concentration was greater in DF-derived than in plasma-derived samples. A total of 13 variants were detected: 11 vs. 1 were exclusive for DF relative to the plasma source, and 1 was shared between the two body fluids. According to the four-tier systems, 10 clinical tier-I-II (76.9%), 1 tier-III (7.7%), and 2 tier-IV (15.4%) variants were identified. Notably, the 11 tier-I-III variants were exclusively found in DF-derived cfDNA from five patients with biliopancreatic cancers, and were detected in seven genes (KRAS, TP53, BRAF, CDKN2A, RNF43, GNAS, and PIK3CA); 82% of the tier-I-III variants had a low abundance, with a VAF < 6%. The mutational profiling of DF seems to be a reliable and promising tool for identifying cancer-associated alterations in malignant cancers of the biliopancreatic tract.
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Affiliation(s)
- Francesca Tavano
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Anna Latiano
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Orazio Palmieri
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Domenica Gioffreda
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Tiziana Latiano
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Annamaria Gentile
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Matteo Tardio
- Department of Surgery, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Tiziana Pia Latiano
- Department of Oncology, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Marco Gentile
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Fulvia Terracciano
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
| | - Francesco Perri
- Division of Gastroenterology and Endoscopy, Fondazione IRCCS “Casa Sollievo della Sofferenza” Hospital, Viale Cappuccini 1, 71013 San Giovanni Rotondo, FG, Italy
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Liu Y, Liu J, Zhang S, Wang J, Sun Z, Sun H, Yang Y, Zheng G, Huang Y, Li M, Zhang Z, Xiao J, Zeng C, Sun C, Qu H, Fang X. A panel sequencing dataset of peripheral blood gene variations in pan-cancer. Sci Data 2024; 11:805. [PMID: 39033182 PMCID: PMC11271301 DOI: 10.1038/s41597-024-03620-6] [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: 10/25/2023] [Accepted: 07/08/2024] [Indexed: 07/23/2024] Open
Abstract
Circulating cell-free DNA (cfDNA) in the peripheral blood is a promising biomarker for cancer diagnosis and prognosis. Somatic mutations identified in cancers have been used to detect therapeutic targets for clinical transformation and individualize drug selection, while germline variants can predict a patient's risk of developing cancer and drug sensitivity. However, no platform has been developed to analyze, calculate, integrate, and friendly visualize these pan-cancer cfDNA mutations deeply. In this work, we performed panel sequencing encompassing 1,115 cancer-related genes across 16,659 cancer patients, spanning 27 cancer types. We detected 496 germline variants in leukocytes and 11,232 somatic mutations in the cfDNA of all patients. CPGV (Cancer Peripheral blood Gene Variations), a database constructed from this dataset, is the first pan-cancer cfDNA database that encompasses somatic mutations, germline variants, and further comparative analyses of mutations across different cancer types. It bears great promise to serve as a valuable resource for cancer research.
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Affiliation(s)
- Yanxia Liu
- China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Liu
- Yantai Yuhuangding Hospital, Yantai, 264000, China
| | - Shouwei Zhang
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Jinyue Wang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- National Genomics Data Center, China National Center for Bioinformation, Beijing, 100101, China
| | - Zhihong Sun
- Yantai Yuhuangding Hospital, Yantai, 264000, China
| | - Huaibo Sun
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Ying Yang
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Guangmin Zheng
- China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Huang
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Meng Li
- China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China
| | - Zhaojun Zhang
- China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China
| | - Jingfa Xiao
- China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- National Genomics Data Center, China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Changqing Zeng
- China National Center for Bioinformation, Beijing, 100101, China
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Hongzhu Qu
- China National Center for Bioinformation, Beijing, 100101, China.
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China.
| | - Xiangdong Fang
- China National Center for Bioinformation, Beijing, 100101, China.
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing, 100101, China.
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Erice E, Mitxelena-Iribarren O, Arana S, Lawrie CH, Mujika M. Efficient enrichment of free target sequences in an integrated microfluidic device for point-of-care detection systems. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 61:102771. [PMID: 38960366 DOI: 10.1016/j.nano.2024.102771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/07/2024] [Accepted: 06/23/2024] [Indexed: 07/05/2024]
Abstract
Nucleic acid biomarker detection has great importance in the diagnosis of disease, the monitoring of disease progression and the classification of patients according to treatment decision making. Nucleic acid biomarkers found in the blood of patients have generated a lot of interest due to the possibility of being detected non-invasively which makes them ideal for monitoring and screening tests and particularly amenable to point-of-care (POC) or self-testing. A major challenge to POC molecular diagnostics is the need to enrich the target to optimise detection. In this work, we describe a microfabricated device for the enrichment of short dsDNA target sequences, which is especially valuable for potential detection methods, as it improves the probability of effectively detecting the target in downstream analyses. The device integrated a heating element and a temperature sensor with a microfluidic chamber to carry out the denaturation of the dsDNA combined with blocking-probes to enrich the target. This procedure was validated by fluorescence resonance energy transfer (FRET) technique, labelling DNA with a fluorophore and a quencher. As proof of concept, a 23-mer long dsDNA sequence corresponding to the L858R mutation of the EGFR gene was used. The qualitative results obtained determined that the most optimal blocking rate was obtained with the incorporation of 11/12-mer blocking-probes at a total concentration of 6 μM. This device is a powerful DNA preparation tool, which is an indispensable initial step for subsequent detection of sequences via nucleic acid hybridisation methods.
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Affiliation(s)
- Elisa Erice
- CEIT-Basque Research and Technology Alliance (BRTA), Manuel Lardizabal 15, 20018 Donostia, San Sebastián, Spain; Universidad de Navarra, Tecnun, Manuel Lardizabal 13, 20018 Donostia, San Sebastián, Spain.
| | - Oihane Mitxelena-Iribarren
- CEIT-Basque Research and Technology Alliance (BRTA), Manuel Lardizabal 15, 20018 Donostia, San Sebastián, Spain; Universidad de Navarra, Tecnun, Manuel Lardizabal 13, 20018 Donostia, San Sebastián, Spain; Group of Bioengineering in Regeneration and Cancer, Biogipuzkoa Health Research Institute, San Sebastian, Spain
| | - Sergio Arana
- CEIT-Basque Research and Technology Alliance (BRTA), Manuel Lardizabal 15, 20018 Donostia, San Sebastián, Spain; Universidad de Navarra, Tecnun, Manuel Lardizabal 13, 20018 Donostia, San Sebastián, Spain
| | - Charles H Lawrie
- Molecular Oncology Group, Biogipuzkoa Health Research Institute, San Sebastian, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; Sino-Swiss Institute of Advanced Technology (SSIAT), University of Shanghai, Shanghai, China; Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Maite Mujika
- CEIT-Basque Research and Technology Alliance (BRTA), Manuel Lardizabal 15, 20018 Donostia, San Sebastián, Spain; Universidad de Navarra, Tecnun, Manuel Lardizabal 13, 20018 Donostia, San Sebastián, Spain
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Lippert J, Smith G, Appenzeller S, Landwehr LS, Prete A, Steinhauer S, Asia M, Urlaub H, Elhassan YS, Kircher S, Arlt W, Fassnacht M, Altieri B, Ronchi CL. Circulating cell-free DNA-based biomarkers for prognostication and disease monitoring in adrenocortical carcinoma. Eur J Endocrinol 2024; 190:234-247. [PMID: 38451242 DOI: 10.1093/ejendo/lvae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 01/11/2024] [Accepted: 02/16/2024] [Indexed: 03/08/2024]
Abstract
OBJECTIVE Adrenocortical carcinoma (ACC) is a rare aggressive cancer with heterogeneous behaviour. Disease surveillance relies on frequent imaging, which comes with significant radiation exposure. The aim of the study was to investigate the role of circulating cell-free DNA (ccfDNA)-related biomarkers (BMs) for prognostication and monitoring of ACC. DESIGN AND METHODS We investigated 34 patients with ACC and 23 healthy subjects (HSs) as controls. Circulating cell-free DNA was extracted by commercial kits and ccfDNA concentrations were quantified by fluorimeter (BM1). Targeted sequencing was performed using a customized panel of 27 ACC-specific genes. Leucocyte DNA was used to discriminate somatic variants (BM2), while tumour DNA was sequenced in 22/34 cases for comparison. Serial ccfDNA samples were collected during follow-up in 19 ACC patients (median period 9 months) and analysed in relationship with standard radiological imaging. RESULTS Circulating cell-free DNA concentrations were higher in ACC than HS (mean ± SD, 1.15 ± 1.56 vs 0.05 ± 0.05 ng/µL, P < .0001), 96% of them being above the cut-off of 0.146 ng/µL (mean HS + 2 SD, positive BM1). At ccfDNA sequencing, 47% of ACC showed at least 1 somatic mutation (positive BM2). A combined ccfDNA-BM score was strongly associated with both progression-free and overall survival (hazard ratio [HR] = 2.63; 95% CI, 1.13-6.13; P = .010, and HR = 5.98; 95% CI, 2.29-15.6; P = .0001, respectively). During disease monitoring, positive BM2 showed the best specificity (100%) and sensitivity (67%) to detect ACC recurrence or progress compared with BM1. CONCLUSION ccfDNA-related BMs are frequently detected in ACC patients and represent a promising, minimally invasive tool to predict clinical outcome and complement surveillance imaging. Our findings will be validated in a larger cohort of ACCs with long-term follow-up.
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Affiliation(s)
- Juliane Lippert
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, University of Wuerzburg, 97080 Wuerzburg, Germany
- Institute of Human Genetics, University of Wuerzburg, 97070 Wuerzburg, Germany
| | - Gabrielle Smith
- Institute of Metabolism and System Research, University of Birmingham, B152TT Birmingham, United Kingdom
| | - Silke Appenzeller
- Core Unit Bioinformatics, Comprehensive Cancer Center Mainfranken, University of Wuerzburg, 97070 Wuerzburg, Germany
| | - Laura-Sophie Landwehr
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Alessandro Prete
- Institute of Metabolism and System Research, University of Birmingham, B152TT Birmingham, United Kingdom
- Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, B152TT Birmingham, United Kingdom
- NIHR Birmingham Biomedical Research Centre, University of Birmingham, University Hospitals Birmingham NHS Foundation Trust, B152GW Birmingham, United Kingdom
| | - Sonja Steinhauer
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Miriam Asia
- Endocrine Department, Queen Elizabeth Hospital Birmingham NHS Trust, B152GW Birmingham, United Kingdom
| | - Hanna Urlaub
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Yasir S Elhassan
- Institute of Metabolism and System Research, University of Birmingham, B152TT Birmingham, United Kingdom
- Endocrine Department, Queen Elizabeth Hospital Birmingham NHS Trust, B152GW Birmingham, United Kingdom
| | - Stefan Kircher
- Department of Pathology, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Wiebke Arlt
- Institute of Metabolism and System Research, University of Birmingham, B152TT Birmingham, United Kingdom
- MRC Laboratory of Medical Sciences, W120TN London, United Kingdom
| | - Martin Fassnacht
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Barbara Altieri
- Division of Endocrinology and Diabetes, Department of Medicine, University Hospital, University of Wuerzburg, 97080 Wuerzburg, Germany
| | - Cristina L Ronchi
- Institute of Metabolism and System Research, University of Birmingham, B152TT Birmingham, United Kingdom
- Centre for Endocrinology, Diabetes and Metabolism (CEDAM), Birmingham Health Partners, B152TT Birmingham, United Kingdom
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Yang Q, Zhu X, Liu Y, He Z, Xu H, Zheng H, Huang Z, Wang D, Lin X, Guo P, Chen H. Reduced representative methylome profiling of cell-free DNA for breast cancer detection. Clin Epigenetics 2024; 16:33. [PMID: 38414041 PMCID: PMC10898043 DOI: 10.1186/s13148-024-01641-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/06/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Whole-genome methylation sequencing of cfDNA is not cost-effective for tumor detection. Here, we introduce reduced representative methylome profiling (RRMP), which employs restriction enzyme for depletion of AT-rich sequence to achieve enrichment and deep sequencing of CG-rich sequences. METHODS We first verified the ability of RRMP to enrich CG-rich sequences using tumor cell genomic DNA and analyzed differential methylation regions between tumor cells and normal whole blood cells. We then analyzed cfDNA from 29 breast cancer patients and 27 non-breast cancer individuals to detect breast cancer by building machine learning models. RESULTS RRMP captured 81.9% CpG islands and 75.2% gene promoters when sequenced to 10 billion base pairs, with an enrichment efficiency being comparable to RRBS. RRMP allowed us to assess DNA methylation changes between tumor cells and whole blood cells. Applying our approach to cfDNA from 29 breast cancer patients and 27 non-breast cancer individuals, we developed machine learning models that could discriminate between breast cancer and non-breast cancer controls (AUC = 0.85), suggesting possibilities for truly non-invasive cancer detection. CONCLUSIONS We developed a new method to achieve reduced representative methylome profiling of cell-free DNA for tumor detection.
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Affiliation(s)
- Qingmo Yang
- The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Xingqiang Zhu
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Yulu Liu
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Zhi He
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Huan Xu
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Hailing Zheng
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Zhiming Huang
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Dan Wang
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Xiaofang Lin
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Ping Guo
- Xiamen Huazao Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China.
| | - Hongliang Chen
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China.
- School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
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Li P, Liu Z. Glycan-specific molecularly imprinted polymers towards cancer diagnostics: merits, applications, and future perspectives. Chem Soc Rev 2024; 53:1870-1891. [PMID: 38223993 DOI: 10.1039/d3cs00842h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Aberrant glycans are a hallmark of cancer states. Notably, emerging evidence has demonstrated that the diagnosis of cancers with tumour-specific glycan patterns holds great potential to address unmet medical needs, especially in improving diagnostic sensitivity and selectivity. However, despite vast glycans having been identified as potent markers, glycan-based diagnostic methods remain largely limited in clinical practice. There are several reasons that prevent them from reaching the market, and the lack of anti-glycan antibodies is one of the most challenging hurdles. With the increasing need for accelerating the translational process, numerous efforts have been made to find antibody alternatives, such as lectins, boronic acids and aptamers. However, issues concerning affinity, selectivity, stability and versatility are yet to be fully addressed. Molecularly imprinted polymers (MIPs), synthetic antibody mimics with tailored cavities for target molecules, hold the potential to revolutionize this dismal progress. MIPs can bind a wide range of glycan markers, even those without specific antibodies. This capacity effectively broadens the clinical applicability of glycan-based diagnostics. Additionally, glycoform-resolved diagnosis can also be achieved through customization of MIPs, allowing for more precise diagnostic applications. In this review, we intent to introduce the current status of glycans as potential biomarkers and critically evaluate the challenges that hinder the development of in vitro diagnostic assays, with a particular focus on glycan-specific recognition entities. Moreover, we highlight the key role of MIPs in this area and provide examples of their successful use. Finally, we conclude the review with the remaining challenges, future outlook, and emerging opportunities.
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Affiliation(s)
- Pengfei Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China.
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, Jiangsu, China.
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Paul T, Palaniyandi K, Gnanasampanthapandian D. Therapeutic Approaches to Increase the Survival Rate of Cancer Patients in the Younger and Older Population. Curr Aging Sci 2024; 17:16-30. [PMID: 38062658 DOI: 10.2174/0118746098241507231127114248] [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: 01/25/2023] [Revised: 06/25/2023] [Accepted: 09/22/2023] [Indexed: 05/18/2024]
Abstract
Various developments have been observed in the treatment of cancer patients, such as higher survival rates and better treatment outcomes. However, expecting similar outcomes in older patients remains a challenge. The main reason for this conclusion is the exclusion of older people from clinical trials for cancer drugs, as well as other factors, such as comorbidity, side effects, age-related frailties and their willingness to undergo multiple treatments. However, the discovery of new techniques and drug combinations has led to a significant improvement in the survival of the elderly population after the onset of the disease. On the other hand, cancer treatments have not become more complex for the younger population when compared to the older population, as the younger population tends to respond well to treatment trials and their physiological conditions are stable in response to treatments. In summary, this review correlates recent cancer treatment strategies and the corresponding responses and survival outcomes of older and younger patients.
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Affiliation(s)
- Tharrun Paul
- Cancer Science Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu, India
| | - Kanagaraj Palaniyandi
- Cancer Science Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu, India
| | - Dhanavathy Gnanasampanthapandian
- Cancer Science Laboratory, Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, 603203, Chengalpattu, India
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Nie C, Shaw I, Chen C. Application of microfluidic technology based on surface-enhanced Raman scattering in cancer biomarker detection: A review. J Pharm Anal 2023; 13:1429-1451. [PMID: 38223444 PMCID: PMC10785256 DOI: 10.1016/j.jpha.2023.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 01/16/2024] Open
Abstract
With the continuous discovery and research of predictive cancer-related biomarkers, liquid biopsy shows great potential in cancer diagnosis. Surface-enhanced Raman scattering (SERS) and microfluidic technology have received much attention among the various cancer biomarker detection methods. The former has ultrahigh detection sensitivity and can provide a unique fingerprint. In contrast, the latter has the characteristics of miniaturization and integration, which can realize accurate control of the detection samples and high-throughput detection through design. Both have the potential for point-of-care testing (POCT), and their combination (lab-on-a-chip SERS (LoC-SERS)) shows good compatibility. In this paper, the basic situation of circulating proteins, circulating tumor cells, exosomes, circulating tumor DNA (ctDNA), and microRNA (miRNA) in the diagnosis of various cancers is reviewed, and the detection research of these biomarkers by the LoC-SERS platform in recent years is described in detail. At the same time, the challenges and future development of the platform are discussed at the end of the review. Summarizing the current technology is expected to provide a reference for scholars engaged in related work and interested in this field.
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Affiliation(s)
- Changhong Nie
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, China
| | - Ibrahim Shaw
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, China
| | - Chuanpin Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, China
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Salimi M, Rastegarpouyani S. E74-like Factor 5 Promoter Methylation in Circulating Tumor DNA as a Potential Prognostic Marker in Breast Cancer Patients. Asian Pac J Cancer Prev 2023; 24:4035-4041. [PMID: 38156835 PMCID: PMC10909102 DOI: 10.31557/apjcp.2023.24.12.4035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 12/19/2023] [Indexed: 01/03/2024] Open
Abstract
BACKGROUND Epigenetic alternations, such as DNA methylation, play a crucial role in breast tumor initiation and progression. The identification of noninvasive prognostic biomarkers has great importance in cancer management. Methylated cell-free DNA (cfDNA), circulating in the blood as a convenient tumor-associated DNA marker, can be used as a minimally invasive cancer biomarker. This study aimed to evaluate the promoter methylation status of E74-like factor 5 (ELF5) tumor suppressor gene in both tumors and plasma cell-free DNA of 80 breast cancer patients, compared with normal controls. METHODS Plasma cfDNA concentrations were measured using quantitative real-time PCR, and methylation pattern in the ELF5 gene promoter region was performed using methylation-specific polymerase chain reaction (MS-PCR) technique. RESULTS The data revealed a statistically significant increase in cfDNA concentrations in breast cancer patients, particularly in those with higher stages of the disease, triple-negative status, and metastasis (p<0.001). ELF5 promoter region hypermethylation was observed in 70% of breast cancer patients in both plasma cfDNA and tumor tissues. Notably, all patients with lymph node involvement and distant metastatic exhibited promoter hypermethylation in the ELF5 gene. CONCLUSION Our findings suggest that ELF5 promoter methylation in circulating DNA could serve as a potential non-invasive prognostic molecular marker in breast cancer patients. However, further studies are warranted to evaluate its diagnostic value.
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Affiliation(s)
- Mahdieh Salimi
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
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Zelli V, Manno A, Compagnoni C, Ibraheem RO, Zazzeroni F, Alesse E, Rossi F, Arbib C, Tessitore A. Classification of tumor types using XGBoost machine learning model: a vector space transformation of genomic alterations. J Transl Med 2023; 21:836. [PMID: 37990214 PMCID: PMC10664515 DOI: 10.1186/s12967-023-04720-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023] Open
Abstract
BACKGROUND Machine learning (ML) represents a powerful tool to capture relationships between molecular alterations and cancer types and to extract biological information. Here, we developed a plain ML model aimed at distinguishing cancer types based on genetic lesions, providing an additional tool to improve cancer diagnosis, particularly for tumors of unknown origin. METHODS TCGA data from 9,927 samples spanning 32 different cancer types were downloaded from cBioportal. A vector space model type data transformation technique was designed to build consistently homogeneous new datasets containing, as predictive features, calls for somatic point mutations and copy number variations at chromosome arm-level, thus allowing the use of the XGBoost classifier models. Considering the imbalance in the dataset, due to large difference in the number of cases for each tumor, two preprocessing strategies were considered: i) setting a percentage cut-off threshold to remove less represented cancer types, ii) dividing cancer types into different groups based on biological criteria and training a specific XGBoost model for each of them. The performance of all trained models was mainly assessed by the out-of-sample balanced accuracy (BACC) and the AUC scores. RESULTS The XGBoost classifier achieved the best performance (BACC 77%; AUC 97%) on a dataset containing the 10 most represented tumor types. Moreover, dividing the 18 most represented cancers into three different groups (endocrine-related carcinomas, other carcinomas and other cancers),such analysis models achieved 78%, 71% and 86% BACC, respectively, with AUC scores greater than 96%. In addition, the model capable of linking each group to a specific cancer type reached 81% BACC and 94% AUC. Overall, the diagnostic potential of our model was comparable/higher with respect to others already described in literature and based on similar molecular data and ML approaches. CONCLUSIONS A boosted ML approach able to accurately discriminate different cancer types was developed. The methodology builds datasets simpler and more interpretable than the original data, while keeping enough information to accurately train standard ML models without resorting to sophisticated Deep Learning architectures. In combination with histopathological examinations, this approach could improve cancer diagnosis by using specific DNA alterations, processed by a replicable and easy-to-use automated technology. The study encourages new investigations which could further increase the classifier's performance, for example by considering more features and dividing tumors into their main molecular subtypes.
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Affiliation(s)
- Veronica Zelli
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100, L'Aquila, Italy
- Center for Molecular Diagnostics and Advanced Therapies, University of L'Aquila, Via Petrini, 67100, L'Aquila, Italy
| | - Andrea Manno
- Department of Information Engineering, Computer Science and Mathematics, Center of Excellence DEWS, University of L'Aquila, 67100, L'Aquila, Italy
| | - Chiara Compagnoni
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Rasheed Oyewole Ibraheem
- Department of Information Engineering, Computer Science and Mathematics, Center of Excellence DEWS, University of L'Aquila, 67100, L'Aquila, Italy
| | - Francesca Zazzeroni
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Edoardo Alesse
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100, L'Aquila, Italy
| | - Fabrizio Rossi
- Department of Information Engineering, Computer Science and Mathematics, Center of Excellence DEWS, University of L'Aquila, 67100, L'Aquila, Italy
| | - Claudio Arbib
- Department of Information Engineering, Computer Science and Mathematics, Center of Excellence DEWS, University of L'Aquila, 67100, L'Aquila, Italy
| | - Alessandra Tessitore
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, 67100, L'Aquila, Italy.
- Center for Molecular Diagnostics and Advanced Therapies, University of L'Aquila, Via Petrini, 67100, L'Aquila, Italy.
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Surappa S, Multani P, Parlatan U, Sinawang PD, Kaifi J, Akin D, Demirci U. Integrated "lab-on-a-chip" microfluidic systems for isolation, enrichment, and analysis of cancer biomarkers. LAB ON A CHIP 2023; 23:2942-2958. [PMID: 37314731 PMCID: PMC10834032 DOI: 10.1039/d2lc01076c] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The liquid biopsy has garnered considerable attention as a complementary clinical tool for the early detection, molecular characterization and monitoring of cancer over the past decade. In contrast to traditional solid biopsy techniques, liquid biopsy offers a less invasive and safer alternative for routine cancer screening. Recent advances in microfluidic technologies have enabled handling of liquid biopsy-derived biomarkers with high sensitivity, throughput, and convenience. The integration of these multi-functional microfluidic technologies into a 'lab-on-a-chip' offers a powerful solution for processing and analyzing samples on a single platform, thereby reducing the complexity, bio-analyte loss and cross-contamination associated with multiple handling and transfer steps in more conventional benchtop workflows. This review critically addresses recent developments in integrated microfluidic technologies for cancer detection, highlighting isolation, enrichment, and analysis strategies for three important sub-types of cancer biomarkers: circulating tumor cells, circulating tumor DNA and exosomes. We first discuss the unique characteristics and advantages of the various lab-on-a-chip technologies developed to operate on each biomarker subtype. This is then followed by a discussion on the challenges and opportunities in the field of integrated systems for cancer detection. Ultimately, integrated microfluidic platforms form the core of a new class of point-of-care diagnostic tools by virtue of their ease-of-operation, portability and high sensitivity. Widespread availability of such tools could potentially result in more frequent and convenient screening for early signs of cancer at clinical labs or primary care offices.
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Affiliation(s)
- Sushruta Surappa
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
| | - Priyanka Multani
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
| | - Ugur Parlatan
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
| | - Prima Dewi Sinawang
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Jussuf Kaifi
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65212, USA
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA
| | - Demir Akin
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
- Center for Cancer Nanotechnology Excellence for Translational Diagnostics (CCNE-TD), School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Utkan Demirci
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
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12
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Gopal P, Ahmed Z, Venkata Ravi Kant V, Rao GV, Rebala P. Circulating tumor DNA for monitoring colorectal cancer: A prospective observational study to assess the presence of methylated SEPT9 and VIM promoter genes and its role as a biomarker in colorectal cancer management. Turk J Surg 2023; 39:107-114. [PMID: 38026919 PMCID: PMC10681108 DOI: 10.47717/turkjsurg.2023.6038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/23/2023] [Indexed: 12/01/2023]
Abstract
Objectives Methylation status of Septin9 (SEPT9) and vimentin (VIM) genes in circulating tumor DNA of colorectal cancer (CRC) patients is a promising bio-marker for the early detection of CRC. The aim of the present study was to identify the methylation status in promoter regions of the SEPT9 and VIM genes in a cohort of Indian patients with biopsy proven colorectal cancer. Material and Methods Forty-five consecutive patients of colorectal cancer were recruited. 10 mL venous samples were collected from each patient and processed for isolation of cell-free DNA, bisulfite conversion of cell-free DNA, polymerase chain reaction (PCR) amplification and detection of SEPT9 and VIM genes. Results Partial methylation in vimentin was present in 42.22% of the patients and 57.78% showed no methylation and none of the tumors had complete methylation. Only three (6.66%) patients showed complete methylation patterns in SEPT9 and the remaining 42 (93.33%) tumors showed partial methylation. Considering the two genes together, only three (6.66%) out of 45 showed complete methylation. The association of methylation patterns in both genes (complete, partial, and no methylation) with sex, age, T stage, N stage, M stage, CEA, histology, and location (right or left colon) were explored and none of these parameters were statistically significant. Conclusion In our study, only 6.66% CRC patients showed hypermethylation and there was no association of methylation patterns in the both genes (complete, partial, and no methylation) with any of the parameters like age, sex, TNM stage, CEA, and histology.
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Affiliation(s)
- Puviarasan Gopal
- Department of Surgical Gastroenterology, Asian Institute of Gastroenterology, Hyderabad, India
| | - Zeeshan Ahmed
- Department of Surgical Gastroenterology, Asian Institute of Gastroenterology, Hyderabad, India
| | | | - G V Rao
- Department of Surgical Gastroenterology, Asian Institute of Gastroenterology, Hyderabad, India
| | - Pradeep Rebala
- Department of Surgical Gastroenterology, Asian Institute of Gastroenterology, Hyderabad, India
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Latifi-Navid S, Safaralizadeh R, Wei L. Editorial: Circulating tumor DNA in cancer: a role as a response and monitoring "next-generation" biomarker in cancer therapy. Front Oncol 2023; 13:1210866. [PMID: 37324007 PMCID: PMC10267465 DOI: 10.3389/fonc.2023.1210866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 05/23/2023] [Indexed: 06/17/2023] Open
Affiliation(s)
- Saeid Latifi-Navid
- Department of Biology, Faculty of Sciences, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Reza Safaralizadeh
- Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Lixuan Wei
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
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14
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Hazra RS, Khan MRH, Kale N, Tanha T, Khandare J, Ganai S, Quadir M. Bioinspired Materials for Wearable Devices and Point-of-Care Testing of Cancer. ACS Biomater Sci Eng 2023; 9:2103-2128. [PMID: 35679474 PMCID: PMC9732150 DOI: 10.1021/acsbiomaterials.1c01208] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Wearable, point-of-care diagnostics, and biosensors are on the verge of bringing transformative changes in detection, management, and treatment of cancer. Bioinspired materials with new forms and functions have frequently been used, in both translational and commercial spaces, to fabricate such diagnostic platforms. Engineered from organic or inorganic molecules, bioinspired systems are naturally equipped with biorecognition and stimuli-sensitive properties. Mechanisms of action of bioinspired materials are deeply connected with thermodynamically or kinetically controlled self-assembly at the molecular and supramolecular levels. Thus, integration of bioinspired materials into wearable devices, either as triggers or sensors, brings about unique device properties usable for detection, capture, or rapid readout for an analyte of interest. In this review, we present the basic principles and mechanisms of action of diagnostic devices engineered from bioinspired materials, describe current advances, and discuss future trends of the field, particularly in the context of cancer.
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Affiliation(s)
- Raj Shankar Hazra
- Materials and Nanotechnology Program, North Dakota State University, Fargo, ND 58108, United States
| | - Md Rakib Hasan Khan
- Biomedical Engineering Program, North Dakota State University, Fargo, ND 58108, United States
| | - Narendra Kale
- Actorius Innovations and Research Pvt. Ltd., Pune, 411057 India
| | - Tabassum Tanha
- Genomics and Bioinformatics Program, North Dakota State University, Fargo, ND 58108, United States
| | - Jayant Khandare
- Actorius Innovations and Research Pvt. Ltd., Pune, 411057 India
- School of Pharmacy, Dr. Vishwananth Karad MIT World Peace University, Kothrud, Pune 411038, India
- School of Consciousness, MIT WPU, Kothrud, Pune 411038, India
| | - Sabha Ganai
- Division of Surgical Oncology, Sanford Research, Fargo, North Dakota 58122, United States
- Complex General Surgical Oncology, University of North Dakota, Grand Forks, ND 58202, United States
| | - Mohiuddin Quadir
- Materials and Nanotechnology Program, North Dakota State University, Fargo, ND 58108, United States
- Biomedical Engineering Program, North Dakota State University, Fargo, ND 58108, United States
- Department of Coatings and Polymeric Materials, North Dakota State University, Fargo, ND 58108, United States
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15
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Abou-Zeid A, Hashad D, Baess A, Mosaad M, Tayae E. HOXA9 gene promotor methylation and copy number variation of SOX2 and HV2 genes in cell free DNA: A potential diagnostic panel for non-small cell lung cancer. BMC Cancer 2023; 23:329. [PMID: 37038139 PMCID: PMC10088126 DOI: 10.1186/s12885-023-10793-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/30/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Most cases of lung cancer are diagnosed at advanced stage. Detection of genetic and epigenetic markers in cell-free DNA (cfDNA) is a promising tool for the diagnosis of lung cancer at an early stage. The aim of this study was to identify non-invasive diagnostic markers in cell free DNA (cfDNA) for non-small cell lung cancer (NSCLC) as it is the most common type of lung cancer. METHODS We investigated the cfDNA HOXA9 gene promotor methylation by pyrosequencing. Copy number variation of SOX2 and HV2 genes were detected by real-time PCR in cfDNA extracted from plasma samples of 25 newly diagnosed NSCLC patients and 25 age and sex matched controls. RESULTS Methylation level of HOXA9 was significantly higher in NSCLC patients than controls (p > 0.001). SOX2 showed significantly higher CNV and HV2 showed lower CNV in patients than controls (p > 0.001, p = 0.001 respectively). Receiver Operating Characteristic (ROC) curve analysis for HOXA9 methylation, SOX2 CNV and HV2 CNV showed a discrimination power of 79.4%, 80% and 77.5% respectively and the area under the curve for the combined analysis of the three genes was 0.958 with 88% sensitivity and 100% specificity. CONCLUSIONS In this study, we suggest a potentially diagnostic panel that may help in detection of lung cancer with high sensitivity and specificity using cell free DNA. This Panel included HOXA9 gene methylation and the CNV of SOX2 and HV2 genes.
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Affiliation(s)
- Abla Abou-Zeid
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Doaa Hashad
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Ayman Baess
- Department of Chest Diseases, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Mai Mosaad
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Eman Tayae
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Alexandria University, Alexandria, Egypt.
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16
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Park W, Maeng SW, Mok JW, Choi M, Cha HJ, Joo CK, Hahn SK. Hydrogel Microneedles Extracting Exosomes for Early Detection of Colorectal Cancer. Biomacromolecules 2023; 24:1445-1452. [PMID: 36908257 DOI: 10.1021/acs.biomac.2c01449] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
There are several methods for early diagnosis of tumors, such as detecting circulating tumor DNAs, detecting circulating tumor cells, or imaging with tumor-targeting contrast agents. However, these assays are time-consuming and may cause patient discomfort during the biopsy collecting process. Here, we develop a facile method for early diagnosis of tumors by extracting exosomes from interstitial fluid (ISF) using hydrogel microneedles (MNs). The hydrogel MNs expand in the skin to absorb the ISF, and the tumor exosomes contained in the ISF bind with the glypican-1 antibodies inside the hydrogel of MNs. After removing the hydrogel on the MNs, exosomes are separately purified from the ISF to analyze tumor-related biomarkers. Finally, colorectal cancer can be diagnosed by ELISA for the colorectal cancer-induced model mice. This noninvasive hydrogel MN system to obtain the exosome samples would play an important role in early cancer diagnosis.
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Affiliation(s)
- Wonchan Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Seong-Woo Maeng
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jee Won Mok
- CK St. Mary's Eye Center, CK Building, 559, Gangnam-daero, Seocho-gu, Seoul 06531, Republic of Korea
| | - Minji Choi
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Hyung Joon Cha
- Department of Chemical Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Choun-Ki Joo
- CK St. Mary's Eye Center, CK Building, 559, Gangnam-daero, Seocho-gu, Seoul 06531, Republic of Korea
| | - Sei Kwang Hahn
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
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Metastatic Melanoma: Liquid Biopsy as a New Precision Medicine Approach. Int J Mol Sci 2023; 24:ijms24044014. [PMID: 36835424 PMCID: PMC9962821 DOI: 10.3390/ijms24044014] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
Precision medicine has driven a major change in the treatment of many forms of cancer. The discovery that each patient is different and each tumor mass has its own characteristics has shifted the focus of basic and clinical research to the singular individual. Liquid biopsy (LB), in this sense, presents new scenarios in personalized medicine through the study of molecules, factors, and tumor biomarkers in blood such as circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), exosomes and circulating tumor microRNAs (ct-miRNAs). Moreover, its easy application and complete absence of contraindications for the patient make this method applicable in a great many fields. Melanoma, given its highly heterogeneous characteristics, is a cancer form that could significantly benefit from the information linked to liquid biopsy, especially in the treatment management. In this review, we will focus our attention on the latest applications of liquid biopsy in metastatic melanoma and possible developments in the clinical setting.
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18
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Chen G, Zhang J, Fu Q, Taly V, Tan F. Integrative analysis of multi-omics data for liquid biopsy. Br J Cancer 2023; 128:505-518. [PMID: 36357703 PMCID: PMC9938261 DOI: 10.1038/s41416-022-02048-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
The innovation of liquid biopsy holds great potential to revolutionise cancer management through early diagnosis and timely treatment of cancer. Integrative analysis of different tumour-derived omics data (such as genomics, epigenetics, fragmentomics, and proteomics) from body fluids for cancer detection and monitoring could outperform the analysis of single modality data alone. In this review, we focussed on the discussion of early cancer detection and molecular residual disease surveillance based on multi-omics data of blood. We summarised diverse types of tumour-derived components, current popular platforms for profiling cancer-associated signals, machine learning approaches for joint analysis of liquid biopsy data, as well as multi-omics-based early detection of cancers, molecular residual disease monitoring, and treatment response surveillance. We also discussed the challenges and future directions of multi-omics-based liquid biopsy. With the development of both experimental protocols and computational methods dedicated to liquid biopsy, the implementation of multi-omics strategies into the clinical workflow will likely benefit the clinical management of cancers including decision-making guidance and patient outcome improvement.
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Affiliation(s)
- Geng Chen
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, 200443, Shanghai, China.
- Center for Bioinformatics and Computational Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China.
| | - Jing Zhang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, 200443, Shanghai, China
| | - Qiaoting Fu
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, 200443, Shanghai, China
| | - Valerie Taly
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe labélisée Ligue Nationale contre le cancer, Centre de Recherche des Cordeliers, Paris, France.
| | - Fei Tan
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, 200443, Shanghai, China.
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, 200443, Shanghai, China.
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Age alone is not a barrier to efficacy of cytoreductive surgery and hyperthermic intraperitoneal chemotherapy for colorectal peritoneal metastases: analysis of 1138 patients from the UK and Ireland Colorectal Peritoneal Metastases Registry. Br J Cancer 2023; 128:42-47. [PMID: 36347966 DOI: 10.1038/s41416-022-02037-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/11/2022] [Accepted: 10/18/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The management of colorectal peritoneal metastases continues to be a challenge but recent evidence suggests cytoreductive surgery (CRS) with hyperthermic intraperitoneal chemotherapy (HIPEC) can improve survival. Uncertainty about the relationship between age and tumour biology makes patient selection challenging particularly when reported procedure related morbidity is high and impact on survival outcomes unknown. The UK and Ireland Colorectal Peritoneal Metastases Registry was reviewed to assess the influence of age on efficacy of CRS and HIPEC. METHODS A review of outcomes from the UK and Ireland Colorectal Peritoneal Metastases Registry was performed. Data from 2000 to 2021 were included from five centres in the UK and Ireland, and the cohort were sub-divided into three age groups; <45 years, 45-65 years and >65 years old. Primarily, we examined post-operative morbidity and survival outcomes across the three age groups. In addition, we examined the impact that the completeness of cytoreduction, nodal status, or adverse pathological features had on long-term survival. RESULTS During the study period, 1138 CPM patients underwent CRS HIPEC. 202 patients(17.8%) were <45 years, 549 patients(48.2%) aged 45-65 years and 387 patients(34%) >65 years. Overall, median length of surgery (CRS and HIPEC), median PCI score and rate of HIPEC administration was similar in all three groups, as was overall rates of major morbidity and/or mortality. Complete cytoreduction rates (CC0) were similar across the three cohorts; 77%, 80.6% and 81%, respectively. Median overall survival for all patients was 38 months following complete cytoreduction. CONCLUSION Age did not appear to influence morbidity or long-term survival following CRS and HIPEC. When complete cytoreduction is achieved survival outcomes are good. The addition of HIPEC can be performed safely and may reduce local recurrence within the peritoneum.
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20
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Jia LL, Zhao JX, Zhao LP, Tian JH, Huang G. Current status and quality of radiomic studies for predicting KRAS mutations in colorectal cancer patients: A systematic review and meta‑analysis. Eur J Radiol 2023; 158:110640. [PMID: 36525703 DOI: 10.1016/j.ejrad.2022.110640] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 11/13/2022] [Accepted: 11/28/2022] [Indexed: 12/14/2022]
Abstract
PURPOSE The purpose of this study was to evaluate the methodological quality of radiomics-based studies for noninvasive, preoperative prediction of Kirsten rat sarcoma (KRAS) mutations in patients with colorectal cancer; furthermore, we systematically evaluate the diagnostic accuracy of predicting models. METHODS We systematically searched PubMed, Embase, Cochrane Library and Web of Science databases up to 20 April 2022 for eligible studies. The methodological quality of included studies was assessed using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) and Radiomics Quality Score (RQS) tools. A meta-analysis of studies on the prediction of KRAS status in colorectal cancer patients was performed. RESULT Twenty-nine studies were identified in the systematic review, including three studies on the prediction of KRAS status in colorectal cancer liver metastases. All studies had an average RQS score of 9.55 (26.5% of the total score), ranging from 3 to 17. Most studies demonstrated a low or unclear risk of bias in the domains of QUADAS-2. Nineteen studies were included in the meta-analysis, mostly imaged with magnetic resonance imaging (MRI), followed by computed tomography (CT), positron emission tomography-CT (PET/CT). With pooled sensitivity, specificity and area under the curve (AUC) of the training cohorts were 0.80(95% confidence interval(CI), 0.75-0.84), 0.80(95% CI, 0.74-0.85) and 0.87(95% CI, 0.84-0.90),respectively. The pooled sensitivity, specificity, and AUC for the validation cohorts (13 studies) were 0.78(95% CI, 0.71-0.84), 0.84(95% CI, 0.74-0.90), and 0.86(95% CI, 0.83-0.89), respectively. CONCLUSION Radiomics is a potential noninvasive technology that has a moderate preoperative diagnosis and prediction effect on KRAS mutations. However, it has not been implemented as a clinical decision-making tool. Future researchers should pay more attention to the methodological quality of the study and further externally validate the model using multicenter datasets.
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Affiliation(s)
- Lu-Lu Jia
- First Clinical School of Medicine, Gansu University of Chinese Medicine, Lanzhou 73000, China.
| | - Jian-Xin Zhao
- First Clinical School of Medicine, Gansu University of Chinese Medicine, Lanzhou 73000, China.
| | - Lian-Ping Zhao
- Department of Radiology, Gansu Provincial Hospital, Lanzhou 730000, China.
| | - Jin-Hui Tian
- Evidence-Based Medicine Center, School of Basic Medical Sciences, Lanzhou University, Lanzhou 730000, China.
| | - Gang Huang
- Department of Radiology, Gansu Provincial Hospital, Lanzhou 730000, China.
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O'Keefe CM, Wang THJ. Fabrication of Multilayer Microfluidic Arrays for Passive, Efficient DNA Trapping and Profiling. Methods Mol Biol 2023; 2679:315-322. [PMID: 37300626 DOI: 10.1007/978-1-0716-3271-0_22] [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] [Indexed: 06/12/2023]
Abstract
Trace amounts of cell-free DNA containing cancer-specific biomarkers can be found in blood plasma. Detection of these biomarkers holds tremendous potential for applications such as noninvasive cancer diagnostics and therapeutic monitoring. However, such DNA molecules are extremely rare, and a typical patient blood sample may only contain a few copies. Here we describe the fabrication and operation of a microfluidic device to efficiently trap single DNA molecules into chambers for detection of tumor-specific biomarkers through a passive, geometric manipulation strategy.
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Affiliation(s)
- Christine M O'Keefe
- Johns Hopkins University, Whiting School of Engineering, Department of Biomedical Engineering, Baltimore, MD, USA
| | - Tza-Huei Jeff Wang
- Johns Hopkins University, Whiting School of Engineering, Department of Biomedical Engineering, Baltimore, MD, USA.
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22
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Uthamacumaran A, Abdouh M, Sengupta K, Gao ZH, Forte S, Tsering T, Burnier JV, Arena G. Machine intelligence-driven classification of cancer patients-derived extracellular vesicles using fluorescence correlation spectroscopy: results from a pilot study. Neural Comput Appl 2022. [DOI: 10.1007/s00521-022-08113-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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Introduction of Nanomaterials to Biosensors for Exosome Detection: Case Study for Cancer Analysis. BIOSENSORS 2022; 12:bios12080648. [PMID: 36005042 PMCID: PMC9405681 DOI: 10.3390/bios12080648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/04/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
Abstract
Exosomes have been gaining attention for early cancer diagnosis owing to their biological functions in cells. Several studies have reported the relevance of exosomes in various diseases, including pancreatic cancer, retroperitoneal fibrosis, obesity, neurodegenerative diseases, and atherosclerosis. Particularly, exosomes are regarded as biomarkers for cancer diagnosis and can be detected in biofluids, such as saliva, urine, peritoneal fluid, and blood. Thus, exosomes are advantageous for cancer liquid biopsies as they overcome the current limitations of cancer tissue biopsies. Several studies have reported methods for exosome isolation, and analysis for cancer diagnosis. However, further clinical trials are still required to determine accurate exosome concentration quantification methods. Recently, various biosensors have been developed to detect exosomal biomarkers, including tumor-derived exosomes, nucleic acids, and proteins. Among these, the exact quantification of tumor-derived exosomes is a serious obstacle to the clinical use of liquid biopsies. Precise detection of exosome concentration is difficult because it requires clinical sample pretreatment. To solve this problem, the use of the nanobiohybrid material-based biosensor provides improved sensitivity and selectivity. The present review will discuss recent progress in exosome biosensors consisting of nanomaterials and biomaterial hybrids for electrochemical, electrical, and optical-based biosensors.
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24
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de Nóbrega M, Dos Reis MB, Pereira ÉR, de Souza MF, de Syllos Cólus IM. The potential of cell-free and exosomal microRNAs as biomarkers in liquid biopsy in patients with prostate cancer. J Cancer Res Clin Oncol 2022; 148:2893-2910. [PMID: 35922694 DOI: 10.1007/s00432-022-04213-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/14/2022] [Indexed: 12/19/2022]
Abstract
PURPOSE Prostate cancer (PCa) is the 4th most diagnosed cancer and the 8th leading cause of cancer-related death worldwide. Currently, clinical risk stratification models including factors like PSA levels, Gleason score, and digital rectal examination are used for this purpose. There is a need for novel biomarkers that can distinguish between indolent and aggressive pathology and reduce the risk of overdiagnosis/overtreatment. Liquid biopsy has a non-invasive character, can lead to less morbidity and provide new biomarkers, such as miRNAs, that regulate diverse important cellular processes. Here, we report an extended revision about the role of cell-free and exosomal miRNAs (exomiRNAs) as biomarkers for screening, diagnosis, prognosis, or treatment of PCa. METHODS A comprehensive review of the published literature was conducted focusing on the usefulness, advantages, and clinical applications of cell-free and exomiRNAs in serum and plasma. Using PubMed database 53 articles published between 2012 and 2021 were selected and discussed from the perspective of their use as diagnostic, prognostic and therapeutic biomarkers for PCa. RESULTS We identify 119 miRNAs associated with PCa development and the cell-free and exosomal miR-21, miR-141, miR-200c, and miR-375 were consistently associated with progression in multiple cohorts/studies. However, standardized experimental procedures, and well-defined and clinically relevant cohort studies are urgently needed to confirm the biomarker potential of cell-free and exomiRNAs in serum or plasma. CONCLUSION Cell-free and exomiRNAs in serum or plasma are promising tools for be used as non-invasive biomarkers for diagnostic, prognosis, therapy improvement and clinical outcome prediction in PCa patients.
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Affiliation(s)
- Monyse de Nóbrega
- Department of General Biology, Laboratory of Mutagenesis and Oncogenetics, Center of Biologic Sciences, State University of Londrina, Rodovia Celso Garcia Cid, PR-445, Km 380-University Campus, Londrina, PR, CEP 86057-970, Brazil
| | - Mariana Bisarro Dos Reis
- Barretos Cancer Hospital (Molecular Oncology Research Center), Barretos, SP, CEP 14784-400, Brazil
| | - Érica Romão Pereira
- Department of General Biology, Laboratory of Mutagenesis and Oncogenetics, Center of Biologic Sciences, State University of Londrina, Rodovia Celso Garcia Cid, PR-445, Km 380-University Campus, Londrina, PR, CEP 86057-970, Brazil
| | - Marilesia Ferreira de Souza
- Department of General Biology, Laboratory of Mutagenesis and Oncogenetics, Center of Biologic Sciences, State University of Londrina, Rodovia Celso Garcia Cid, PR-445, Km 380-University Campus, Londrina, PR, CEP 86057-970, Brazil
| | - Ilce Mara de Syllos Cólus
- Department of General Biology, Laboratory of Mutagenesis and Oncogenetics, Center of Biologic Sciences, State University of Londrina, Rodovia Celso Garcia Cid, PR-445, Km 380-University Campus, Londrina, PR, CEP 86057-970, Brazil.
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25
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Qayyumi B, Bharde A, Aland G, D'Souza A, Jayant S, Singh N, Tripathi S, Badave R, Kale N, Singh B, Arora S, Gore I, Singh A, Vasudevan A, Prabhash K, Khandare J, Chaturvedi P. Circulating tumor cells as a predictor for poor prognostic factors and overall survival in treatment naïve oral squamous cell carcinoma patients. Oral Surg Oral Med Oral Pathol Oral Radiol 2022; 134:73-83. [PMID: 35595620 DOI: 10.1016/j.oooo.2022.02.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 01/10/2022] [Accepted: 02/28/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE The aim of this study was to investigate the presence of circulating tumor cells (CTCs) and their correlation with prognostic factors and clinical outcomes in treatment-naive patients with oral squamous cell carcinoma. STUDY DESIGN CTCs were isolated using OncoDiscover technique from presurgically obtained peripheral blood of 152 patients with treatment naïve oral squamous cell carcinoma. Sensitivity analysis was performed by including 40 healthy controls. CTCs cutoff values for clinicopathologic factors were obtained from receiver operating characteristic curves. Multivariate models determined the significance of CTC as independent variables. Kaplan-Meier analysis differentiated in overall survival between CTC values corresponding to the stage. RESULTS Sensitivity, specificity, and accuracy of CTC detection were 94.32%, 98%, and 95.17%, respectively. Platform differentiated true positives at >3.5 CTCs (P < .00001). CTCs above 20.5 were suggestive of nodal metastasis (P < .0001) with a linear trend for detecting occult metastasis (P = .061). Early and advanced stages could be differentiated by >13.5 CTCs (P < .0001). Elevated CTCs were significantly associated with extranodal extension (>21.45 CTCs, P = .025), perineural invasion (>19.35 CTCs, P = .049), and depth of invasion (>12.5 CTCs, P = .0038). Median survival was reduced by 19 months when CTCs were >13. CONCLUSIONS Preoperative CTC levels demonstrated a strong correlation with adverse clinicopathology factors and suggested its role as a sensitive prognostic marker to predict survival outcome and disease progress.
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Affiliation(s)
- Burhanuddin Qayyumi
- Department of Head and Neck Surgical Oncology, Tata Memorial Hospital, Mumbai, India; Homi Bhabha National Institute, Mumbai, India
| | - Atul Bharde
- Department of Microbiology, Savitribai Phule Pune University, Pune, India
| | | | - Alain D'Souza
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Sreeja Jayant
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Nitin Singh
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Swati Tripathi
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Reecha Badave
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Narendra Kale
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Balram Singh
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Smriti Arora
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Isha Gore
- Actorius Innovations and Research Pvt. Ltd., Pune, India
| | - Arjun Singh
- Department of Head and Neck Surgical Oncology, Tata Memorial Hospital, Mumbai, India; Homi Bhabha National Institute, Mumbai, India
| | | | - Kumar Prabhash
- Department of Head and Neck Surgical Oncology, Tata Memorial Hospital, Mumbai, India; Homi Bhabha National Institute, Mumbai, India
| | - Jayant Khandare
- Actorius Innovations and Research Pvt. Ltd., Pune, India; Actorius Innovations and Research Co, Simi Valley, CA, USA; OneCell Diagnostics Inc, Cupertino, CA, USA; OneCell Diagnostics Pvt. Ltd., Pune, India.
| | - Pankaj Chaturvedi
- Department of Head and Neck Surgical Oncology, Tata Memorial Hospital, Mumbai, India; Homi Bhabha National Institute, Mumbai, India.
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26
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Patel A, Patel S, Patel P, Tanavde V. Saliva Based Liquid Biopsies in Head and Neck Cancer: How Far Are We From the Clinic? Front Oncol 2022; 12:828434. [PMID: 35387114 PMCID: PMC8977527 DOI: 10.3389/fonc.2022.828434] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/25/2022] [Indexed: 12/24/2022] Open
Abstract
Head and neck cancer (HNC) remains to be a major cause of mortality worldwide because of confounding factors such as late-stage tumor diagnosis, loco-regional aggressiveness and distant metastasis. The current standardized diagnostic regime for HNC is tissue biopsy which fails to determine the thorough tumor dynamics. Therefore, due to the ease of collection, recent studies have focused on the utility of saliva based liquid biopsy approach for serial sampling, early diagnosis, prognosis, longitudinal monitoring of disease progression and treatment response in HNC patients. Saliva collection is convenient, non-invasive, and pain-free and offers repetitive sampling along with real time monitoring of the disease. Moreover, the detection, isolation and analysis of tumor-derived components such as Circulating Tumor Nucleic Acids (CTNAs), Extracellular Vesicles (EVs), Circulating Tumor Cells (CTCs) and metabolites from saliva can be used for genomic and proteomic examination of HNC patients. Although, these circulatory biomarkers have a wide range of applications in clinical settings, no validated data has yet been established for their usage in clinical practice for HNC. Improvements in isolation and detection technologies and next-generation sequencing analysis have resolved many technological hurdles, allowing a wide range of saliva based liquid biopsy application in clinical backgrounds. Thus, in this review, we discussed the rationality of saliva as plausible biofluid and clinical sample for diagnosis, prognosis and therapeutics of HNC. We have described the molecular components of saliva that could mirror the disease status, recent outcomes of salivaomics associated with HNC and current technologies which have the potential to improve the clinical value of saliva in HNC.
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Affiliation(s)
- Aditi Patel
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Shanaya Patel
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Parina Patel
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India
| | - Vivek Tanavde
- Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Ahmedabad, India.,Bioinformatics Institute, Agency for Science Technology and Research (ASTAR), Singapore, Singapore
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27
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Hayashi T, Yoshida Y, Yamada T, Tanaka K, Shimaoka H, Kajitani R, Munechika T, Nagano H, Matsumoto Y, Komono A, Sakamoto R, Aisu N, Yoshimatsu G, Yoshimura F, Hasegawa S. Relationship between perioperative oncological evaluation and recurrence using circulating tumor DNA with KRAS mutation in patients with colorectal cancer. Cancer Med 2022; 11:3126-3135. [PMID: 35312176 PMCID: PMC9385586 DOI: 10.1002/cam4.4677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 03/04/2022] [Indexed: 12/29/2022] Open
Abstract
Background The detection of circulating tumor DNA (ctDNA) in colorectal cancer (CRC) by liquid biopsy may have prognostic information. In this perioperative study, we evaluate if there is a relationship between mutant allele frequency (MAF) of Kirsten rat sarcoma viral oncogene homolog (KRAS) and tumor recurrence and how that could be useful in the early detection of recurrence. Methods Among 304 cases of colorectal cancer surgery, ctDNA was sampled from the perioperative blood of 84 patients with CRC with KRAS mutation (exon 4 p.A146T, exon 4 p.A146V, exon 2 p.G12A, exon 2 p.G12C, exon 2 p.G12D, exon 2 p.G12S, exon 2 p.G12V, exon 2 p.G13D, exon 3 p.Q61H) and analyzed using the digital polymerase chain reaction system. The median observation period was 26 months. Results Although the relationship between the perioperative MAF of KRAS and recurrence was not proved, tumor diameter, tumor depth, and stage were correlated with the preoperative MAF of KRAS (p = 0.034, p = 0.002, p = 0.008). However, tumor diameter, tumor depth, and stage did not correlate with MAF of KRAS at postoperative day 30. Conclusions In this study, pathological tumor size, tumor depth, and stage were correlated with preoperative MAF of KRAS, but it was unreliable to predict recurrence by detection of ctDNA with KRAS mutation in the perioperative period of colorectal surgery.
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Affiliation(s)
- Takaomi Hayashi
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Yoichiro Yoshida
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Teppei Yamada
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Keita Tanaka
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Hideki Shimaoka
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Ryuji Kajitani
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Taro Munechika
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Hideki Nagano
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Yoshiko Matsumoto
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Akira Komono
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Ryohei Sakamoto
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Naoya Aisu
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Gumpei Yoshimatsu
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Fumihiro Yoshimura
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
| | - Suguru Hasegawa
- Department of Gastroenterological Surgery, Fukuoka University Faculty of Medicine, Fukuoka, Japan
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28
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Lone SN, Nisar S, Masoodi T, Singh M, Rizwan A, Hashem S, El-Rifai W, Bedognetti D, Batra SK, Haris M, Bhat AA, Macha MA. Liquid biopsy: a step closer to transform diagnosis, prognosis and future of cancer treatments. Mol Cancer 2022; 21:79. [PMID: 35303879 PMCID: PMC8932066 DOI: 10.1186/s12943-022-01543-7] [Citation(s) in RCA: 217] [Impact Index Per Article: 108.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/21/2022] [Indexed: 02/07/2023] Open
Abstract
Over the past decade, invasive techniques for diagnosing and monitoring cancers are slowly being replaced by non-invasive methods such as liquid biopsy. Liquid biopsies have drastically revolutionized the field of clinical oncology, offering ease in tumor sampling, continuous monitoring by repeated sampling, devising personalized therapeutic regimens, and screening for therapeutic resistance. Liquid biopsies consist of isolating tumor-derived entities like circulating tumor cells, circulating tumor DNA, tumor extracellular vesicles, etc., present in the body fluids of patients with cancer, followed by an analysis of genomic and proteomic data contained within them. Methods for isolation and analysis of liquid biopsies have rapidly evolved over the past few years as described in the review, thus providing greater details about tumor characteristics such as tumor progression, tumor staging, heterogeneity, gene mutations, and clonal evolution, etc. Liquid biopsies from cancer patients have opened up newer avenues in detection and continuous monitoring, treatment based on precision medicine, and screening of markers for therapeutic resistance. Though the technology of liquid biopsies is still evolving, its non-invasive nature promises to open new eras in clinical oncology. The purpose of this review is to provide an overview of the current methodologies involved in liquid biopsies and their application in isolating tumor markers for detection, prognosis, and monitoring cancer treatment outcomes.
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Affiliation(s)
- Saife N Lone
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, Jammu & Kashmir, India
| | - Sabah Nisar
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Tariq Masoodi
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Mayank Singh
- Department of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Arshi Rizwan
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
| | - Sheema Hashem
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Wael El-Rifai
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Veterans Affairs, Miami Healthcare System, Miami, FL, USA
| | - Davide Bedognetti
- Cancer Research Department, Research Branch, Sidra Medicince, Doha, Qatar
- Department of Internal Medicine and Medical Specialities, University of Genova, Genova, Italy
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, NE 68198, Omaha, USA
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha, NE 68198, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, University of Nebraska Medical Center, NE 68198, Omaha, USA
| | - Mohammad Haris
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar
- Laboratory Animal Research Center, Qatar University, Doha, Qatar
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Ajaz A Bhat
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar.
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, (IUST), 192122, Awantipora, Jammu & Kashmir, India.
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29
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Breadner DA, Vincent MD, Correa R, Black M, Warner A, Sanatani M, Bhat V, Morris C, Jones G, Allan A, Palma DA, Raphael J. Exploitation of treatment induced tumor lysis to enhance the sensitivity of ctDNA analysis: A first-in-human pilot study. Lung Cancer 2022; 165:145-151. [PMID: 35124411 DOI: 10.1016/j.lungcan.2022.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/30/2021] [Accepted: 01/19/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Blood-based liquid biopsies examining circulating tumour DNA (ctDNA) have increasing applications in non-small cell lung cancer (NSCLC). Limitations in sensitivity remain a barrier to ctDNA replacing tissue-based testing. We hypothesized that testing immediately after starting treatment would yield an increased abundance of ctDNA in plasma because of tumor lysis, allowing for the detection of genetic alterations that were occult in baseline testing. METHODS Three prospective cohorts of patients with stage III/IV NSCLC were enrolled. Cohort 1 (C1) contained patients starting platinum doublet chemoradiation (n = 10) and cohort 2 (C2) initiating platinum doublet cytotoxic chemotherapy ± immunotherapy (n = 10). Cohort 3 (C3) contained patients receiving palliative radiation. Two baseline samples were collected. In C1 and C2, subsequent samples were collected 3, 6, 24 and 48 h post initiation of chemotherapy. Patients in C3 had samples collected immediately prior to the next three radiotherapy fractions. Samples were analyzed for ctDNA using the 36-gene amplicon-based NGS Inivata InVisionFirst®-Lung assay. RESULTS A total of 40 patients were enrolled. Detectable ctDNA was present at baseline in 32 patients (80%), 4 additional patients (50%) had detectable ctDNA in post-treatment samples. Seven patients with detectable ctDNA at baseline (23%) had new genetic alterations detected in post-treatment samples. Mutant molecule numbers increased with treatment in 24 of 31 (77%) pts with detectable ctDNA. ctDNA levels peaked a median of 7 h (IQR:2-26 h) after the initiation of chemotherapy and a median of 2 days (IQR:1-3 days) after radiation was commenced. CONCLUSION ctDNA levels increase in the hours to days after starting treatment. ctDNA testing in the acute post-treatment phase can yield results that were not evident in pre-treatment testing. Application of this principle could improve ctDNA utility as an alternate to tissue-based testing and improve sensitivity for the detection of treatment-resistant clones.(NCT03986463).
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Affiliation(s)
- Daniel A Breadner
- Division of Medical Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada.
| | - Mark D Vincent
- Division of Medical Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
| | - Rohann Correa
- Division of Radiation Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
| | - Morgan Black
- Division of Medical Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
| | - Andrew Warner
- Division of Radiation Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
| | - Michael Sanatani
- Division of Medical Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
| | - Vasudeva Bhat
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, 1151 Richmond St, N6A 5C1 London, Ontario, Canada
| | - Clive Morris
- Inivata Inc., 7020 Kit Creek Road, Suite 140, Research Triangle Park, 27560, NC, United States
| | - Greg Jones
- Inivata Inc., 7020 Kit Creek Road, Suite 140, Research Triangle Park, 27560, NC, United States
| | - Alison Allan
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, 1151 Richmond St, N6A 5C1 London, Ontario, Canada
| | - David A Palma
- Division of Radiation Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
| | - Jacques Raphael
- Division of Medical Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
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Naoumi N, Michaelidou K, Papadakis G, Simaiaki AE, Fernández R, Calero M, Arnau A, Tsortos A, Agelaki S, Gizeli E. Acoustic Array Biochip Combined with Allele-Specific PCR for Multiple Cancer Mutation Analysis in Tissue and Liquid Biopsy. ACS Sens 2022; 7:495-503. [PMID: 35073481 DOI: 10.1021/acssensors.1c02245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Regular screening of point mutations is of importance to cancer management and treatment selection. Although techniques like next-generation sequencing and digital polymerase chain reaction (PCR) are available, these are lacking in speed, simplicity, and cost-effectiveness. The development of alternative methods that can detect the extremely low concentrations of the target mutation in a fast and cost-effective way presents an analytical and technological challenge. Here, an approach is presented where for the first time an allele-specific PCR (AS-PCR) is combined with a newly developed high fundamental frequency quartz crystal microbalance array as biosensor for the amplification and detection, respectively, of cancer point mutations. Increased sensitivity, compared to fluorescence detection of the AS-PCR amplicons, is achieved through energy dissipation measurement of acoustically "lossy" liposomes binding to surface-anchored dsDNA targets. The method, applied to the screening of BRAF V600E and KRAS G12D mutations in spiked-in samples, was shown to be able to detect 1 mutant copy of genomic DNA in an excess of 104 wild-type molecules, that is, with a mutant allele frequency (MAF) of 0.01%. Moreover, validation of tissue and plasma samples obtained from melanoma, colorectal, and lung cancer patients showed excellent agreement with Sanger sequencing and ddPCR; remarkably, the efficiency of this AS-PCR/acoustic methodology to detect mutations in real samples was demonstrated to be below 1% MAF. The combined high sensitivity and technology-readiness level of the methodology, together with the ability for multiple sample analysis (24 array biochip), cost-effectiveness, and compatibility with routine workflow, make this approach a promising tool for implementation in clinical oncology labs for tissue and liquid biopsy.
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Affiliation(s)
- Nikoletta Naoumi
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Kleita Michaelidou
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Vassilika Vouton, Heraklion 70013, Crete, Greece
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Agapi E. Simaiaki
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
| | - Román Fernández
- Advanced Wave Sensors S. L., Algepser 24, Paterna 46988, Spain
- Centro de Investigación e Innovación en Bioingeniería, Universitat Politècnica de València, Valencia 46022, Spain
| | - Maria Calero
- Centro de Investigación e Innovación en Bioingeniería, Universitat Politècnica de València, Valencia 46022, Spain
| | - Antonio Arnau
- Advanced Wave Sensors S. L., Algepser 24, Paterna 46988, Spain
- Centro de Investigación e Innovación en Bioingeniería, Universitat Politècnica de València, Valencia 46022, Spain
| | - Achilleas Tsortos
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
| | - Sofia Agelaki
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Vassilika Vouton, Heraklion 70013, Crete, Greece
- Department of Medical Oncology, University General Hospital of Heraklion, Vassilika Vouton, Crete 71500, Greece
| | - Electra Gizeli
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece
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31
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Rapid Multiplex Strip Test for the Detection of Circulating Tumor DNA Mutations for Liquid Biopsy Applications. BIOSENSORS 2022; 12:bios12020097. [PMID: 35200357 PMCID: PMC8869478 DOI: 10.3390/bios12020097] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/26/2022] [Accepted: 02/01/2022] [Indexed: 01/16/2023]
Abstract
In the era of personalized medicine, molecular profiling of patient tumors has become the standard practice, especially for patients with advanced disease. Activating point mutations of the KRAS proto-oncogene are clinically relevant for many types of cancer, including colorectal cancer (CRC). While several approaches have been developed for tumor genotyping, liquid biopsy has been gaining much attention in the clinical setting. Analysis of circulating tumor DNA for genetic alterations has been challenging, and many methodologies with both advantages and disadvantages have been developed. We here developed a gold nanoparticle-based rapid strip test that has been applied for the first time for the multiplex detection of KRAS mutations in circulating tumor DNA (ctDNA) of CRC patients. The method involved ctDNA isolation, PCR-amplification of the KRAS gene, multiplex primer extension (PEXT) reaction, and detection with a multiplex strip test. We have optimized the efficiency and specificity of the multiplex strip test in synthetic DNA targets, in colorectal cancer cell lines, in tissue samples, and in blood-derived ctDNA from patients with advanced colorectal cancer. The proposed strip test achieved rapid and easy multiplex detection (normal allele and three major single-point mutations) of the clinically relevant KRAS mutations in ctDNA in blood samples of CRC patients with high specificity and repeatability. This multiplex strip test represents a minimally invasive, rapid, low-cost, and promising diagnostic tool for the detection of clinically relevant mutations in cancer patients.
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Teixeira A, Carneiro A, Piairo P, Xavier M, Ainla A, Lopes C, Sousa-Silva M, Dias A, Martins AS, Rodrigues C, Pereira R, Pires LR, Abalde-Cela S, Diéguez L. Advances in Microfluidics for the Implementation of Liquid Biopsy in Clinical Routine. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1379:553-590. [DOI: 10.1007/978-3-031-04039-9_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Mao X, Mei R, Yu S, Shou L, Zhang W, Li K, Qiu Z, Xie T, Sui X. Emerging Technologies for the Detection of Cancer Micrometastasis. Technol Cancer Res Treat 2022; 21:15330338221100355. [PMID: 35903930 PMCID: PMC9340332 DOI: 10.1177/15330338221100355] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The most efficient way to treat tumors is through surgery. However, many cancer
patients have a poor prognosis even when they undergo radical excision at an
early stage. Micrometastasis is one of the most critical factors that induced
this situation. Undetected micrometastasis can lead to the failure of initial
treatment. Therefore, preoperative and intraoperative detection of
micrometastasis could have a significant clinical influence on the prognosis and
optimal therapy for cancer patients. Additionally, to achieve this goal,
researchers have aimed to create more effective detection technologies. Herein,
we classify the currently reported micrometastasis detection technologies,
introduce some representative samples for each technology, including the
limitations, and provide future directions to overcome the limitations.
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Affiliation(s)
- Xuqing Mao
- The Affiliated Hospital of 26494Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China.,School of Pharmacy, 26494Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Ruyi Mei
- The Affiliated Hospital of 26494Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China.,School of Pharmacy, 26494Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Shuxian Yu
- The Affiliated Hospital of 26494Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China.,School of Pharmacy, 26494Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Lan Shou
- The Affiliated Hospital of 26494Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China.,School of Pharmacy, 26494Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Wenzheng Zhang
- The Affiliated Hospital of 26494Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China.,School of Pharmacy, 26494Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Keshuai Li
- The Affiliated Hospital of 26494Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China.,School of Pharmacy, 26494Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Zejing Qiu
- The Affiliated Hospital of 26494Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China.,School of Pharmacy, 26494Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Tian Xie
- The Affiliated Hospital of 26494Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China.,School of Pharmacy, 26494Hangzhou Normal University, Hangzhou, Zhejiang, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, 26494Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Xinbing Sui
- The Affiliated Hospital of 26494Hangzhou Normal University, College of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China.,School of Pharmacy, 26494Hangzhou Normal University, Hangzhou, Zhejiang, China.,Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, 26494Hangzhou Normal University, Hangzhou, Zhejiang, China
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Kepesidis KV, Bozic-Iven M, Huber M, Abdel-Aziz N, Kullab S, Abdelwarith A, Al Diab A, Al Ghamdi M, Hilal MA, Bahadoor MRK, Sharma A, Dabouz F, Arafah M, Azzeer AM, Krausz F, Alsaleh K, Zigman M, Nabholtz JM. Breast-cancer detection using blood-based infrared molecular fingerprints. BMC Cancer 2021; 21:1287. [PMID: 34856945 PMCID: PMC8638519 DOI: 10.1186/s12885-021-09017-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/16/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Breast cancer screening is currently predominantly based on mammography, tainted with the occurrence of both false positivity and false negativity, urging for innovative strategies, as effective detection of early-stage breast cancer bears the potential to reduce mortality. Here we report the results of a prospective pilot study on breast cancer detection using blood plasma analyzed by Fourier-transform infrared (FTIR) spectroscopy - a rapid, cost-effective technique with minimal sample volume requirements and potential to aid biomedical diagnostics. FTIR has the capacity to probe health phenotypes via the investigation of the full repertoire of molecular species within a sample at once, within a single measurement in a high-throughput manner. In this study, we take advantage of cross-molecular fingerprinting to probe for breast cancer detection. METHODS We compare two groups: 26 patients diagnosed with breast cancer to a same-sized group of age-matched healthy, asymptomatic female participants. Training with support-vector machines (SVM), we derive classification models that we test in a repeated 10-fold cross-validation over 10 times. In addition, we investigate spectral information responsible for BC identification using statistical significance testing. RESULTS Our models to detect breast cancer achieve an average overall performance of 0.79 in terms of area under the curve (AUC) of the receiver operating characteristic (ROC). In addition, we uncover a relationship between the effect size of the measured infrared fingerprints and the tumor progression. CONCLUSION This pilot study provides the foundation for further extending and evaluating blood-based infrared probing approach as a possible cross-molecular fingerprinting modality to tackle breast cancer detection and thus possibly contribute to the future of cancer screening.
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Affiliation(s)
- Kosmas V Kepesidis
- Department of Laser Physics, Ludwig Maximilian University of Munich (LMU), Garching, Germany.
- Laboratory for Attosecond Physics, Max Planck Institute of Quantum Optics (MPQ), Garching, Germany.
| | - Masa Bozic-Iven
- Department of Laser Physics, Ludwig Maximilian University of Munich (LMU), Garching, Germany
| | - Marinus Huber
- Department of Laser Physics, Ludwig Maximilian University of Munich (LMU), Garching, Germany
- Laboratory for Attosecond Physics, Max Planck Institute of Quantum Optics (MPQ), Garching, Germany
| | - Nashwa Abdel-Aziz
- Oncology Centre, King Saud University (Medical City), Riyadh, Saudi Arabia
| | - Sharif Kullab
- Oncology Centre, King Saud University (Medical City), Riyadh, Saudi Arabia
| | - Ahmed Abdelwarith
- Oncology Centre, King Saud University (Medical City), Riyadh, Saudi Arabia
| | | | - Mohammed Al Ghamdi
- Oncology Centre, King Saud University (Medical City), Riyadh, Saudi Arabia
| | - Muath Abu Hilal
- Oncology Centre, King Saud University (Medical City), Riyadh, Saudi Arabia
| | - Mohun R K Bahadoor
- Clinical Operations, International Cancer Research Group (ICRG), Sharjah, United Arab Emirates
| | - Abhishake Sharma
- Clinical Operations, International Cancer Research Group (ICRG), Sharjah, United Arab Emirates
| | - Farida Dabouz
- Clinical Operations, International Cancer Research Group (ICRG), Sharjah, United Arab Emirates
| | - Maria Arafah
- Pathology Department, King Saud University, Riyadh, Saudi Arabia
| | - Abdallah M Azzeer
- Physics and Astronomy Department, Attosecond Science Laboratory, King Saud University, Riyadh, Saudi Arabia
| | - Ferenc Krausz
- Department of Laser Physics, Ludwig Maximilian University of Munich (LMU), Garching, Germany
- Laboratory for Attosecond Physics, Max Planck Institute of Quantum Optics (MPQ), Garching, Germany
| | - Khalid Alsaleh
- Oncology Centre, King Saud University (Medical City), Riyadh, Saudi Arabia
| | - Mihaela Zigman
- Department of Laser Physics, Ludwig Maximilian University of Munich (LMU), Garching, Germany
- Laboratory for Attosecond Physics, Max Planck Institute of Quantum Optics (MPQ), Garching, Germany
| | - Jean-Marc Nabholtz
- Department of Laser Physics, Ludwig Maximilian University of Munich (LMU), Garching, Germany
- Oncology Centre, King Saud University (Medical City), Riyadh, Saudi Arabia
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35
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Song HS, Kang DH, Kim H, Ahn TS, Kim TW, Baek MJ. Clinical relevance and prognostic role of preoperative cell-free single-stranded DNA concentrations in colorectal cancer patients. KOREAN JOURNAL OF CLINICAL ONCOLOGY 2021; 17:59-67. [PMID: 36945669 PMCID: PMC9942756 DOI: 10.14216/kjco.21010] [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: 09/09/2021] [Accepted: 11/19/2021] [Indexed: 06/18/2023]
Abstract
PURPOSE Circulating cell-free single-stranded DNA (ccf-ssDNA) is extracellular DNA and it is a useful biomarker for the diagnosis of tumors and predicting the prognosis of tumors. However, the clinical usefulness of ccf-ssDNA in colorectal cancer (CRC) is not well known. Thus, the purpose of this study was to investigate the clinical usefulness of ccf-ssDNA in CRC. METHODS The study was conducted on 44 patients who had undergone surgery for CRC, and ccf-ssDNA level was measured before surgery and statistical analysis was performed on clinical factors. RESULTS The association between ccf-ssDNA level and clinicopathological factors was analyzed and compared, and these factors included age, sex, body mass index, diabetes mellitus, hypertension, tumor markers (carcinoembryonic antigen and carbohydrate antigen 19-9), tumor location, size, stage (TNM), recurrence, and death. The group with a ccf-ssDNA level of ≥7.5 ng/μL had a lower age (P=0.010), and was associated with diabetes mellitus (P=0.037) and lymph node metastasis (P=0.049). Multivariate analysis of disease-free survival showed that lymph node metastasis and ccf-ssDNA level (hazard ratio, 10.011; 95% confidence interval, 2.269-44.175; P=0.002) were independent prognostic factors for recurrence. In terms of overall survival, there were no statistically significant results except for vascular invasion. CONCLUSION This study showed that ccf-ssDNA level in plasma in CRC patients was an independent prognostic factor that could predict recurrence non-invasively. In this regard, further evaluation with a prospective, large sample size study will be needed to obtain additional results.
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Affiliation(s)
- Hyun Soo Song
- Department of Surgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Dong Hyun Kang
- Department of Surgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Hyunjung Kim
- Department of Surgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Tae Sung Ahn
- Department of Surgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
| | - Tae Wan Kim
- Department of Medical Life Science, Soonchunhyang University, Asan, Korea
| | - Moo-Jun Baek
- Department of Surgery, Soonchunhyang University Cheonan Hospital, Cheonan, Korea
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36
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Balakrishnan SG, Ahmad MR, Koloor SSR, Petrů M. Separation of ctDNA by superparamagnetic bead particles in microfluidic platform for early cancer detection. J Adv Res 2021; 33:109-116. [PMID: 34603782 PMCID: PMC8463959 DOI: 10.1016/j.jare.2021.03.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 01/28/2021] [Accepted: 03/01/2021] [Indexed: 11/17/2022] Open
Abstract
Introduction Conventional biopsy, based on extraction from a tumor of a solid tissue specimen requiring needles, endoscopic devices, excision or surgery, is at risk of infection, internal bleeding or prolonged recovery. A non-invasive liquid biopsy is one of the greatest axiomatic consequences of the identification of circulating tumor DNA (ctDNA) as a replaceable surgical tumor bioQpsy technique. Most of the literature studies thus far presented ctDNA detection at almost final stage III or IV of cancer, where the treatment option or cancer management is nearly impossible for diagnosis. Objective Hence, this paper aims to present a simulation study of extraction and separation of ctDNA from the blood plasma of cancer patients of stage I and II by superparamagnetic (SPM) bead particles in a microfluidic platform for early and effective cancer detection. Method The extraction of ctDNA is based on microfiltration of particle size to filter some impurities and thrombocytes plasma, while the separation of ctDNA is based on magnetic manipulation to high yield that can be used for the upstream process. Result Based on the simulation results, an average of 5.7 ng of ctDNA was separated efficiently for every 10 µL blood plasma input and this can be used for early analysis of cancer management. The particle tracing module from COMSOL Multiphysics traced ctDNA with 65.57% of sensitivity and 95.38% of specificity. Conclusion The findings demonstrate the ease of use and versatility of a microfluidics platform and SPM bead particles in clinical research related to the preparation of biological samples. As a sample preparation stage for early analysis and cancer diagnosis, the extraction and separation of ctDNA is most important, so precision medicine can be administered.
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Affiliation(s)
- Samla Gauri Balakrishnan
- Division of Control and Mechatronics Engineering, School of Electrical Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Mohd Ridzuan Ahmad
- Division of Control and Mechatronics Engineering, School of Electrical Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310 Skudai, Johor, Malaysia
| | - Seyed Saeid Rahimian Koloor
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentska 2, 461 17 Liberec, Czech Republic
| | - Michal Petrů
- Institute for Nanomaterials, Advanced Technologies and Innovation, Technical University of Liberec, Studentska 2, 461 17 Liberec, Czech Republic
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37
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Huber M, Kepesidis KV, Voronina L, Fleischmann F, Fill E, Hermann J, Koch I, Milger-Kneidinger K, Kolben T, Schulz GB, Jokisch F, Behr J, Harbeck N, Reiser M, Stief C, Krausz F, Zigman M. Infrared molecular fingerprinting of blood-based liquid biopsies for the detection of cancer. eLife 2021; 10:68758. [PMID: 34696827 PMCID: PMC8547961 DOI: 10.7554/elife.68758] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/13/2021] [Indexed: 01/11/2023] Open
Abstract
Recent omics analyses of human biofluids provide opportunities to probe selected species of biomolecules for disease diagnostics. Fourier-transform infrared (FTIR) spectroscopy investigates the full repertoire of molecular species within a sample at once. Here, we present a multi-institutional study in which we analysed infrared fingerprints of plasma and serum samples from 1639 individuals with different solid tumours and carefully matched symptomatic and non-symptomatic reference individuals. Focusing on breast, bladder, prostate, and lung cancer, we find that infrared molecular fingerprinting is capable of detecting cancer: training a support vector machine algorithm allowed us to obtain binary classification performance in the range of 0.78-0.89 (area under the receiver operating characteristic curve [AUC]), with a clear correlation between AUC and tumour load. Intriguingly, we find that the spectral signatures differ between different cancer types. This study lays the foundation for high-throughput onco-IR-phenotyping of four common cancers, providing a cost-effective, complementary analytical tool for disease recognition.
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Affiliation(s)
- Marinus Huber
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany.,Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
| | - Kosmas V Kepesidis
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany.,Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
| | - Liudmila Voronina
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany
| | - Frank Fleischmann
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany
| | - Ernst Fill
- Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
| | - Jacqueline Hermann
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany
| | - Ina Koch
- Asklepios Biobank for Lung Diseases, Department of Thoracic Surgery, Member of the German Center for Lung Research, DZL, Asklepios Fachkliniken München-Gauting, Munich, Germany
| | - Katrin Milger-Kneidinger
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Internal Medicine V, Munich, Germany
| | - Thomas Kolben
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Obstetrics and Gynecology, Breast Center and Comprehensive Cancer Center (CCLMU), Munich, Germany
| | - Gerald B Schulz
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Urology, Munich, Germany
| | - Friedrich Jokisch
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Urology, Munich, Germany
| | - Jürgen Behr
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Internal Medicine V, Munich, Germany
| | - Nadia Harbeck
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Obstetrics and Gynecology, Breast Center and Comprehensive Cancer Center (CCLMU), Munich, Germany
| | - Maximilian Reiser
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Clinical Radiology, Munich, Germany
| | - Christian Stief
- University Hospital of the Ludwig Maximilians University Munich (LMU), Department of Urology, Munich, Germany
| | - Ferenc Krausz
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany.,Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
| | - Mihaela Zigman
- Ludwig Maximilians University Munich (LMU), Department of Laser Physics, Garching, Germany.,Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
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38
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Ye Y, Tong F, Wang S, Jiang J, Gao J, Liu L, Liu K, Wang F, Wang Z, Ou J, Chen B, Wilson DA, Tu Y, Peng F. Apoptotic Tumor DNA Activated Nanomotor Chemotaxis. NANO LETTERS 2021; 21:8086-8094. [PMID: 34559543 DOI: 10.1021/acs.nanolett.1c02441] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Inspired by the tactic organisms in Nature that can self-direct their movement following environmental stimulus gradient, we proposed a DNase functionalized Janus nanoparticle (JNP) nanomotor system for the first time, which can be powered by ultralow nM to μM levels of DNA. The system exhibited interesting chemotactic behavior toward a DNA richer area, which is physiologically related with many diseases including tumors. In the presence of the subtle DNA gradient generated by apoptotic tumor cells, the cargo loaded nanomotors were able to sense the DNA signal released by the cells and demonstrate directional motion toward tumor cells. For our system, the subtle DNA gradient by a small amount (10 μL) of tumor cells is sufficient to induce the chemotaxis behavior of self-navigating and self-targeting ability of our nanomotor system, which promises to shed new light for tumor diagnosis and therapy.
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Affiliation(s)
- Yicheng Ye
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou 510275, China
| | - Fei Tong
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Shuanghu Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Jiamiao Jiang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Junbin Gao
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Lu Liu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Kun Liu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Fei Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Zhen Wang
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou 510275, China
| | - Juanfeng Ou
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Daniela A Wilson
- Institute for Molecules and Materials, Radboud University, Nijmegen, 6525 AJ, The Netherlands
| | - Yingfeng Tu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou 510515, China
| | - Fei Peng
- School of Materials Science and Engineering, Sun Yat-Sen University, Guangzhou 510275, China
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Greco F, Anastasi F, Pardini LF, Dilillo M, Vannini E, Baroncelli L, Caleo M, McDonnell LA. Longitudinal Bottom-Up Proteomics of Serum, Serum Extracellular Vesicles, and Cerebrospinal Fluid Reveals Candidate Biomarkers for Early Detection of Glioblastoma in a Murine Model. Molecules 2021; 26:5992. [PMID: 34641541 PMCID: PMC8512455 DOI: 10.3390/molecules26195992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/30/2021] [Indexed: 12/04/2022] Open
Abstract
Glioblastoma Multiforme (GBM) is a brain tumor with a poor prognosis and low survival rates. GBM is diagnosed at an advanced stage, so little information is available on the early stage of the disease and few improvements have been made for earlier diagnosis. Longitudinal murine models are a promising platform for biomarker discovery as they allow access to the early stages of the disease. Nevertheless, their use in proteomics has been limited owing to the low sample amount that can be collected at each longitudinal time point. Here we used optimized microproteomics workflows to investigate longitudinal changes in the protein profile of serum, serum small extracellular vesicles (sEVs), and cerebrospinal fluid (CSF) in a GBM murine model. Baseline, pre-symptomatic, and symptomatic tumor stages were determined using non-invasive motor tests. Forty-four proteins displayed significant differences in signal intensities during GBM progression. Dysregulated proteins are involved in cell motility, cell growth, and angiogenesis. Most of the dysregulated proteins already exhibited a difference from baseline at the pre-symptomatic stage of the disease, suggesting that early effects of GBM might be detectable before symptom onset.
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Affiliation(s)
- Francesco Greco
- Institute of Life Sciences, Sant’Anna School of Advanced Studies, 56127 Pisa, Italy;
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
| | - Federica Anastasi
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
- NEST Laboratories, Scuola Normale Superiore, 56127 Pisa, Italy
| | - Luca Fidia Pardini
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Marialaura Dilillo
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
| | - Eleonora Vannini
- CNR, Neuroscience Institute, 56124 Pisa, Italy; (E.V.); (L.B.); (M.C.)
- Fondazione Umberto Veronesi, 20122 Milano, Italy
| | - Laura Baroncelli
- CNR, Neuroscience Institute, 56124 Pisa, Italy; (E.V.); (L.B.); (M.C.)
- IRCCS Fondazione Stella Maris, 56018 Calambrone, Italy
| | - Matteo Caleo
- CNR, Neuroscience Institute, 56124 Pisa, Italy; (E.V.); (L.B.); (M.C.)
- Dipartimento di Scienze Biomediche, Università di Padova, 35131 Padova, Italy
| | - Liam A. McDonnell
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
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40
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Aboelwafa RA, Zakaria NH, Hagazy N, Zaki II, Rady AS, Sharaki OA. Clinical significance of estrogen receptor 1 gene mutations in hormonal resistant breast cancer patients. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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41
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Bridging the Gaps between Circulating Tumor Cells and DNA Methylation in Prostate Cancer. Cancers (Basel) 2021; 13:cancers13164209. [PMID: 34439363 PMCID: PMC8391503 DOI: 10.3390/cancers13164209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/14/2021] [Accepted: 08/18/2021] [Indexed: 01/09/2023] Open
Abstract
Prostate cancer is the second most common male malignancy, with a highly variable clinical presentation and outcome. Therefore, diagnosis, prognostication, and management remain a challenge, as available clinical, imaging, and pathological parameters provide limited risk assessment. Thus, many biomarkers are under study to fill this critical gap, some of them based on epigenetic aberrations that might be detected in liquid biopsies. Herein, we provide a critical review of published data on the usefulness of DNA methylation and circulating tumor cells in diagnosis and treatment decisions in cases of prostate cancer, underlining key aspects and discussing the importance of these advances to the improvement of the management of prostate cancer patients. Using minimally invasive blood tests, the detection of highly specific biomarkers might be crucial for making therapeutic decisions, determining response to specific treatments, and allowing early diagnosis.
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Huang W, Huang H, Zhang S, Wang X, Ouyang J, Lin Z, Chen P. A Novel Diagnosis Method Based on Methylation Analysis of SHOX2 and Serum Biomarker for Early Stage Lung Cancer. Cancer Control 2021; 27:1073274820969703. [PMID: 33167712 PMCID: PMC7791477 DOI: 10.1177/1073274820969703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Objectives: Lung cancer (LC) is often accompanied by significant methylation
abnormalities. This study aimed to develop a decision tree (DT) accompanied
the stature homeobox 2 gene (SHOX2) / prostaglandin E receptor 4 (PTGER4)
gene DNA methylation with traditional tumor marker in the differential
diagnosis of benign and malignant lung nodule. Methods: We performed a study with 104 patients enrolled in the LC group and 36
patients in the benign lung diseases group. All the clinical data of these
patients were collected through electronic medical record. Total Methylation
(TM) status of both SHOX2 and PTGER4 was defined as methylation levels of
SHOX2 plus methylation levels of PTGER4. One-way analysis was used to
compare the concentrations of serum samples and t-test was used to compare
pairwise mean values between groups. Receiver operating curve (ROC) was used
to evaluate the diagnostic value. Furthermore, the strategy was validated in
19 LC patients and 11 patients with benign lung diseases. Results: There were significant differences between the concentration of
neuron-specific enolase (NSE), carcinoembryonic antigen (CEA), cytokeratin
19 fragments (CYFRA21 -1) and the methylation levels of SHOX2, PTGER4 and TM
in lung benign diseases and cancer group. The AUCs of NSE, CEA, CYFRA21 -1,
Methylation SHOX2, Methylation PTGER4 and TM were 0.721 (95% CI:
0.627–0.816), 0.753 (95% CI: 0.673–0.833) and 0.778(95% CI: 0.700–0.856),
0.851(0.786-0.916), 0.847(0.780-0.913) and 0.861(0.800-0.922) respectively.
We developed a DT model with TM and CYFRA21 -1 used in this study, and the
area under the curve (AUC) of DT was 0.921 and the sensitivity up to 0.856.
In the validation cohort, the AUC of SHOX2, PTGER4 and TM was also much
higher than traditional serum markers. Conclusions: Our results indicated that the DT model calculated from the TM and CYFRA21 -1
can accurately classify LC and benign diseases, which showed better
diagnostic performance than traditional serum parameter.
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Affiliation(s)
- Wenhai Huang
- Department of Thoracic Surgery, Jiangmen Centre Hospital, Jiangmen, Guangdong, China
| | - Hao Huang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Shuishen Zhang
- Department of Thoracic Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xueping Wang
- Department of Laboratory Medicine, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Juan Ouyang
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhichao Lin
- Department of Thoracic Surgery, Jiangmen Centre Hospital, Jiangmen, Guangdong, China
| | - Peisong Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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Cervena K, Pardini B, Urbanova M, Vodenkova S, Eva P, Veskrnova V, Levy M, Buchler T, Mokrejs M, Naccarati A, Vodicka P, Vymetalkova V. Mutational landscape of plasma cell-free DNA identifies molecular features associated with therapeutic response in patients with colon cancer. A pilot study. Mutagenesis 2021; 36:358-368. [PMID: 34214148 DOI: 10.1093/mutage/geab024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/30/2021] [Indexed: 12/29/2022] Open
Abstract
Cell-free DNA (cfDNA) has recently been used as a non-invasive diagnostic tool for detecting tumor-specific mutations. cfDNA may also be used for monitoring disease progression and treatment response, but so far researchers focused on one or few genes only. A genomic profile may provide better information on patient prognosis compared to single specific mutations. In this hypothesis-generating study, we profiled by whole exome sequencing serial plasma samples from 10 colon cancer (CC) patients collected before and after 5-fluorouracil-based therapy, and one year after diagnosis to determine alterations associated with treatment response. In parallel, genome profiling was also performed in patients' corresponding tumor tissue to ascertain the molecular landscape of resistant tumors. The mutation concordance between cfDNA and tumor tissue DNA was higher in more advanced tumor stages than in the early stages of the disease. In non-responders, a specific mutation profile was observed in tumor tissues (TPSD1 p.Ala92Thr, CPAMD8 p.Arg341Gln, OBP2A p.ArgTyr123CysHis). A pathogenic APC mutation (p.Ser1315Ter) was detected only in cfDNA of one poor responder one year after the diagnosis and after therapy termination. Another poor responder presented a likely pathogenic TP53 mutation (p.Arg110Pro) in cfDNA of all plasma samplings and in tumor tissue. In conclusion, cfDNA could be used for genetic characterization of CC patients and might be clinically useful for non-invasive therapy response monitoring.
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Affiliation(s)
- Klara Cervena
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
| | - Barbara Pardini
- IIGM Italian Institute for Genomic Medicine, Sp142 Km3.95, 10060 Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Sp142 Km3.95, 10060 Candiolo,Turin, Italy
| | - Marketa Urbanova
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic
| | - Sona Vodenkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, AlejSvobody 76, 323 00 Pilsen, Czech Republic
| | - Pazourkova Eva
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic.,Department of Nephrology, First Faculty of Medicine, Charles University and General Faculty Hospital in Prague, Czech Republic
| | - Veronika Veskrnova
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Videnska 800, 140 59, Prague, Czech Republic
| | - Miroslav Levy
- Department of Surgery, Thomayer University Hospital, Videnska 800, 140 59, Prague, Czech Republic
| | - Tomas Buchler
- Department of Oncology, First Faculty of Medicine, Charles University and Thomayer Hospital, Videnska 800, 140 59, Prague, Czech Republic
| | - Martin Mokrejs
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, AlejSvobody 76, 323 00 Pilsen, Czech Republic
| | - Alessio Naccarati
- IIGM Italian Institute for Genomic Medicine, Sp142 Km3.95, 10060 Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Sp142 Km3.95, 10060 Candiolo,Turin, Italy
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, AlejSvobody 76, 323 00 Pilsen, Czech Republic
| | - Veronika Vymetalkova
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Videnska 1083, 142 20 Prague, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Albertov 4, 128 00 Prague, Czech Republic.,Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, AlejSvobody 76, 323 00 Pilsen, Czech Republic
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Palanca-Ballester C, Rodriguez-Casanova A, Torres S, Calabuig-Fariñas S, Exposito F, Serrano D, Redin E, Valencia K, Jantus-Lewintre E, Diaz-Lagares A, Montuenga L, Sandoval J, Calvo A. Cancer Epigenetic Biomarkers in Liquid Biopsy for High Incidence Malignancies. Cancers (Basel) 2021; 13:cancers13123016. [PMID: 34208598 PMCID: PMC8233712 DOI: 10.3390/cancers13123016] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/04/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Early alterations in cancer include the deregulation of epigenetic events such as changes in DNA methylation and abnormal levels of non-coding (nc)RNAs. Although these changes can be identified in tumors, alternative sources of samples may offer advantages over tissue biopsies. Because tumors shed DNA, RNA, and proteins, biological fluids containing these molecules can accurately reflect alterations found in cancer cells, not only coming from the primary tumor, but also from metastasis and from the tumor microenvironment (TME). Depending on the type of cancer, biological fluids encompass blood, urine, cerebrospinal fluid, and saliva, among others. Such samples are named with the general term "liquid biopsy" (LB). With the advent of ultrasensitive technologies during the last decade, the identification of actionable genetic alterations (i.e., mutations) in LB is a common practice to decide whether or not targeted therapy should be applied. Likewise, the analysis of global or specific epigenetic alterations may also be important as biomarkers for diagnosis, prognosis, and even for cancer drug response. Several commercial kits that assess the DNA promoter methylation of single genes or gene sets are available, with some of them being tested as biomarkers for diagnosis in clinical trials. From the tumors with highest incidence, we can stress the relevance of DNA methylation changes in the following genes found in LB: SHOX2 (for lung cancer); RASSF1A, RARB2, and GSTP1 (for lung, breast, genitourinary and colon cancers); and SEPT9 (for colon cancer). Moreover, multi-cancer high-throughput methylation-based tests are now commercially available. Increased levels of the microRNA miR21 and several miRNA- and long ncRNA-signatures can also be indicative biomarkers in LB. Therefore, epigenetic biomarkers are attractive and may have a clinical value in cancer. Nonetheless, validation, standardization, and demonstration of an added value over the common clinical practice are issues needed to be addressed in the transfer of this knowledge from "bench to bedside".
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Affiliation(s)
- Cora Palanca-Ballester
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- Roche-CHUS Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago (IDIS), 15706 Santiago de Compostela, Spain
| | - Susana Torres
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
| | - Silvia Calabuig-Fariñas
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Pathology, Universitat de València, 46010 Valencia, Spain
| | - Francisco Exposito
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Diego Serrano
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Esther Redin
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Karmele Valencia
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Biochemistry and Genetics, School of Sciences, University of Navarra, 31008 Pamplona, Spain
| | - Eloisa Jantus-Lewintre
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- Molecular Oncology Laboratory, Fundación Hospital General Universitario de Valencia, 46014 Valencia, Spain
- TRIAL Mixed Unit, Centro de Investigación Príncipe Felipe-Fundación para la Investigación del Hospital General Universitario de Valencia, 46014 Valencia, Spain
- Department of Biotechnology, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), 15706 Santiago de Compostela, Spain; (A.R.-C.); (A.D.-L.)
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
| | - Luis Montuenga
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
| | - Juan Sandoval
- Biomarkers and Precision Medicine (UBMP) and Epigenomics Unit, IIS, La Fe, 46026 Valencia, Spain;
- Correspondence: (J.S.); (A.C.)
| | - Alfonso Calvo
- CIBERONC, ISCIII, 28029 Madrid, Spain; (S.T.); (S.C.-F.); (F.E.); (E.R.); (K.V.); (E.J.-L.); (L.M.)
- DISNA and Program in Solid Tumors, Center for Applied Medical Research (CIMA), 31008 Pamplona, Spain;
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, 31008 Pamplona, Spain
- Correspondence: (J.S.); (A.C.)
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45
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Nassar FJ, Msheik ZS, Nasr RR, Temraz SN. Methylated circulating tumor DNA as a biomarker for colorectal cancer diagnosis, prognosis, and prediction. Clin Epigenetics 2021; 13:111. [PMID: 34001239 PMCID: PMC8130320 DOI: 10.1186/s13148-021-01095-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/02/2021] [Indexed: 12/23/2022] Open
Abstract
Worldwide, colorectal cancer (CRC) is a deadly disease whose death rate ranks second among cancers though its incidence ranks third. Early CRC detection is key and is associated with improved survival outcomes. However, existing tests for CRC diagnosis have several weaknesses thus rendering them inefficient. Moreover, reliable prognostic tests that can predict the overall cancer outcome and recurrence of the disease as well as predictive markers that can assess effectiveness of therapy are still lacking. Thus, shifting to noninvasive liquid biopsy or blood-based biomarkers is vital to improving CRC diagnosis, prognosis, and prediction. Methylated circulating tumor DNA (ctDNA) has gained increased attention as a type of liquid biopsy that is tumor-derived fragmented DNA with epigenetic alterations. Methylated ctDNA are more consistently present in blood of cancer patients as compared to mutated ctDNA. Hence, methylated ctDNA serves as a potential biomarker for CRC that is worth investigating. In this review, we explore what has been reported about methylated ctDNA as a biomarker for CRC diagnosis that can distinguish between CRC patients or those having adenoma and healthy controls as validated specifically through ROC curves. We also examine methylated ctDNA as a biomarker for CRC prognosis and prediction as confirmed through robust statistical analyses. Finally, we discuss the major technical challenges that limits the use of methylated ctDNA for clinical application and suggest possible recommendations to enhance its usage.
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Affiliation(s)
- Farah J Nassar
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, P.O. Box: 11-0236, Beirut, Lebanon
| | - Zahraa S Msheik
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, P.O. Box: 11-0236, Beirut, Lebanon
| | - Rihab R Nasr
- Department of Anatomy, Cell Biology and Physiological Sciences, Faculty of Medicine, American University of Beirut, P.O. Box: 11-0236, Beirut, Lebanon.
| | - Sally N Temraz
- Department of Internal Medicine, Faculty of Medicine, American University of Beirut, P.O. Box: 11-0236, Beirut, Lebanon.
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46
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Comprehensive cell type decomposition of circulating cell-free DNA with CelFiE. Nat Commun 2021; 12:2717. [PMID: 33976150 PMCID: PMC8113516 DOI: 10.1038/s41467-021-22901-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 03/23/2021] [Indexed: 12/18/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) in the bloodstream originates from dying cells and is a promising noninvasive biomarker for cell death. Here, we propose an algorithm, CelFiE, to accurately estimate the relative abundances of cell types and tissues contributing to cfDNA from epigenetic cfDNA sequencing. In contrast to previous work, CelFiE accommodates low coverage data, does not require CpG site curation, and estimates contributions from multiple unknown cell types that are not available in external reference data. In simulations, CelFiE accurately estimates known and unknown cell type proportions from low coverage and noisy cfDNA mixtures, including from cell types composing less than 1% of the total mixture. When used in two clinically-relevant situations, CelFiE correctly estimates a large placenta component in pregnant women, and an elevated skeletal muscle component in amyotrophic lateral sclerosis (ALS) patients, consistent with the occurrence of muscle wasting typical in these patients. Together, these results show how CelFiE could be a useful tool for biomarker discovery and monitoring the progression of degenerative disease. Tissue damage and turnover lead to the release of DNA in the blood and can be used to monitor changes in tissue state. Here, the authors developed a tool to accurately estimate the proportion of cell types contributing to cell-free DNA in the blood, with an application to pregnant women and ALS patients.
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47
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Kan CFK, Unis GD, Li LZ, Gunn S, Li L, Soyer HP, Stark MS. Circulating Biomarkers for Early Stage Non-Small Cell Lung Carcinoma Detection: Supplementation to Low-Dose Computed Tomography. Front Oncol 2021; 11:555331. [PMID: 33968710 PMCID: PMC8099172 DOI: 10.3389/fonc.2021.555331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 03/03/2021] [Indexed: 12/13/2022] Open
Abstract
Lung cancer is currently the leading cause of cancer death in both developing and developed countries. Given that lung cancer has poor prognosis in later stages, it is essential to achieve an early diagnosis to maximize patients’ overall survival. Non-small cell lung cancer (NSCLC) is the most common form of primary lung cancer in both smokers and non-smokers. The current standard screening method, low‐dose computed tomography (LDCT), is the only radiological method that demonstrates to have mortality benefits across multiple large randomized clinical trials (RCT). However, these RCTs also found LDCT to have a significant false positive rate that results in unnecessary invasive biopsies being performed. Due to the lack of both sensitive and specific screening methods for the early detection of lung cancer, there is an urgent need for alternative minimally or non-invasive biomarkers that may provide diagnostic, and/or prognostic information. This has led to the identification of circulating biomarkers that can be readily detectable in blood and have been extensively studied as prognosis markers. Circulating microRNA (miRNA) in particular has been investigated for these purposes as an augmentation to LDCT, or as direct diagnosis of lung cancer. There is, however, a lack of consensus across the studies on which miRNAs are the most clinically useful. Besides miRNA, other potential circulating biomarkers include circulating tumor cells (CTCs), circulating tumor DNA (ctDNAs) and non-coding RNAs (ncRNAs). In this review, we provide the current outlook of several of these biomarkers for the early diagnosis of NSCLC.
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Affiliation(s)
- Chin Fung Kelvin Kan
- The University of Queensland, Ochsner Clinical School, Laboratory of Translational Cancer Research, Ochsner Clinic Foundation, New Orleans, LA, United States.,The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, QLD, Australia.,Department of General Surgery, Brigham and Women's Hospital, Boston, MA, United States
| | - Graham D Unis
- The University of Queensland, Ochsner Clinical School, Laboratory of Translational Cancer Research, Ochsner Clinic Foundation, New Orleans, LA, United States.,Department of Medicine, Ochsner Clinic Foundation, New Orleans, LA, United States
| | - Luke Z Li
- The University of Queensland, Ochsner Clinical School, Laboratory of Translational Cancer Research, Ochsner Clinic Foundation, New Orleans, LA, United States.,Department of Medicine, Stamford Hospital, Columbia College of Physicians and Surgeons, Stamford, CT, United States
| | - Susan Gunn
- The University of Queensland, Ochsner Clinical School, Laboratory of Translational Cancer Research, Ochsner Clinic Foundation, New Orleans, LA, United States.,Department of Pulmonary and Critical Care, Ochsner Clinic Foundation, New Orleans, LA, United States
| | - Li Li
- The University of Queensland, Ochsner Clinical School, Laboratory of Translational Cancer Research, Ochsner Clinic Foundation, New Orleans, LA, United States
| | - H Peter Soyer
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, QLD, Australia.,Department of Dermatology, Princess Alexandra Hospital, Brisbane, QLD, Australia
| | - Mitchell S Stark
- The University of Queensland Diamantina Institute, The University of Queensland, Dermatology Research Centre, Brisbane, QLD, Australia
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48
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Profiling Colorectal Cancer in the Landscape Personalized Testing-Advantages of Liquid Biopsy. Int J Mol Sci 2021; 22:ijms22094327. [PMID: 33919272 PMCID: PMC8122648 DOI: 10.3390/ijms22094327] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/14/2021] [Accepted: 04/18/2021] [Indexed: 12/11/2022] Open
Abstract
Drug-specific therapeutic approaches for colorectal cancer (CRC) have contributed to significant improvements in patient health. Nevertheless, there is still a great need to improve the personalization of treatments based on genetic and epigenetic tumor profiles to maximize the quality and efficacy while limiting cytotoxicity. Currently, CEA and CA 19-9 are the only validated blood biomarkers in clinical practice. For this reason, laboratories are trying to identify new specific prognostics and, more importantly, predictive biomarkers for CRC patient profiling. Thus, the unique landscape of personalized biomarker data should have a clinical impact on CRC treatment strategies and molecular genetic screening tests should become the standard method for diagnosing CRC. This review concentrates on recent molecular testing in CRC and discusses the potential modifications in CRC assay methodology with the upcoming clinical application of novel genomic approaches. While mechanisms for analyzing circulating tumor DNA have been proven too inaccurate, detecting and analyzing circulating tumor cells and protein analysis of exosomes represent more promising options. Blood liquid biopsy offers good prospects for the future if the results align with pathologists’ tissue analyses. Overall, early detection, accurate diagnosis and treatment monitoring for CRC with specific markers and targeted molecular testing may benefit many patients.
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49
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Lee YS, Lim K, Minteer SD. Cascaded Biocatalysis and Bioelectrocatalysis: Overview and Recent Advances. Annu Rev Phys Chem 2021; 72:467-488. [DOI: 10.1146/annurev-physchem-090519-050109] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Enzyme cascades are plentiful in nature, but they also have potential in artificial applications due to the possibility of using the target substrate in biofuel cells, electrosynthesis, and biosensors. Cascade reactions from enzymes or hybrid bioorganic catalyst systems exhibit extended substrate range, reaction depth, and increased overall performance. This review addresses the strategies of cascade biocatalysis and bioelectrocatalysis for ( a) CO2 fixation, ( b) high value-added product formation, ( c) sustainable energy sources via deep oxidation, and ( d) cascaded electrochemical enzymatic biosensors. These recent updates in the field provide fundamental concepts, designs of artificial electrocatalytic oxidation-reduction pathways (using a flexible setup involving organic catalysts and engineered enzymes), and advances in hybrid cascaded sensors for sensitive analyte detection.
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Affiliation(s)
- Yoo Seok Lee
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Koun Lim
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Shelley D. Minteer
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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50
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Liquid Biopsies in Head and Neck Cancer: Current State and Future Challenges. Cancers (Basel) 2021; 13:cancers13081874. [PMID: 33919778 PMCID: PMC8070729 DOI: 10.3390/cancers13081874] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 12/11/2022] Open
Abstract
Head and neck cancers are the seventh most frequent malignancy worldwide, consisting of a heterogeneous group of cancers that develop in the oral cavity, pharynx, and larynx, with head and neck squamous cell carcinoma (HNSCC) being the most common pathology. Due to limitations with screening and physical examination, HNSCC often presents in advanced disease states and is thus associated with poor survival. In this setting, liquid biopsies, or obtaining patient bodily fluid samples for cancer diagnosis and prognosis, may play a dramatic role in optimizing care for HNSCC patients. In recent years, there have been dramatic advancements in investigations focused on optimizing and implementing liquid biopsies in general, and specifically for HNSCC patients. Moving forward, there remain significant challenges in liquid biopsy technological development, as well as opportunities for the development of HNSCC liquid biopsy clinical trials and treatment paradigms. In this review, we discuss the current state of liquid biopsy technologies via circulating tumor cells, circulating tumor DNA and exosomes, approaches in head and neck cancer, challenges to optimization and application of liquid biopsies for clinical study, and future prospects for this field of research as it applies to head and neck cancer.
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