Liquid biopsies for omics-based analysis in sentinel mussels

AbstractLiquid biopsy of plasma is a simple and non-invasive technology that holds great promise in biomedical research. It is based on the analysis of nucleic acid-based biomarkers with predictive potential. In the present work, we have combined this concept with the FTA technology for sentinel mussels. We found that hemocytes collected from liquid biopsies can be readily fixed on FTA cards and used for long-term transriptome analysis. We also showed that liquid biopsy is easily adaptable for metagenomic analysis of bacterial profiles of mussels. We finally provide evidence that liquid biopsies contained circulating cell-free DNA (ccfDNA) which can be used as an easily accessible genomic reservoir. Sampling of FTA-fixed circulating nucleic acids is stable at room temperature and does not necessitate a cold-chain protection. It showed comparable performance to frozen samples and is ideally adapted for sampling in remote areas, most notably in polar regions threatened by anthropogenic activities. From an ethical point of view, this minimally-invasive and non-lethal approach further reduces incidental mortality associated with conventional tissue sampling. This liquid biopsy-based approach should thus facilitate biobanking activities and development of omics-based biomarkers in sentinel mussels to assess the quality of marine ecosystems.

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Liquid Biopsy Biomarkers in Bladder Cancer: A Current Need for Patient Diagnosis and Monitoring

International Journal of Molecular Sciences ◽

10.3390/ijms19092514 ◽

2018 ◽

Vol 19 (9) ◽

pp. 2514 ◽

Cited By ~ 18

Author(s):

Iris Lodewijk ◽

Marta Dueñas ◽

Carolina Rubio ◽

Ester Munera-Maravilla ◽

Cristina Segovia ◽

...

Keyword(s):

Bladder Cancer ◽

Liquid Biopsy ◽

Disease Surveillance ◽

Great Promise ◽

Liquid Biopsies ◽

Recurrence Rates ◽

Invasive Approach ◽

Non Invasive ◽

Social Challenge ◽

High Incidence

Bladder Cancer (BC) represents a clinical and social challenge due to its high incidence and recurrence rates, as well as the limited advances in effective disease management. Currently, a combination of cytology and cystoscopy is the routinely used methodology for diagnosis, prognosis and disease surveillance. However, both the poor sensitivity of cytology tests as well as the high invasiveness and big variation in tumour stage and grade interpretation using cystoscopy, emphasizes the urgent need for improvements in BC clinical guidance. Liquid biopsy represents a new non-invasive approach that has been extensively studied over the last decade and holds great promise. Even though its clinical use is still compromised, multiple studies have recently focused on the potential application of biomarkers in liquid biopsies for BC, including circulating tumour cells and DNA, RNAs, proteins and peptides, metabolites and extracellular vesicles. In this review, we summarize the present knowledge on the different types of biomarkers, their potential use in liquid biopsy and clinical applications in BC.

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Precision Medicine for Colorectal Cancer with Liquid Biopsy and Immunotherapy

Cancers ◽

10.3390/cancers13194803 ◽

2021 ◽

Vol 13 (19) ◽

pp. 4803

Author(s):

Satoshi Nagayama ◽

Siew-Kee Low ◽

Kazuma Kiyotani ◽

Yusuke Nakamura

Keyword(s):

Colorectal Cancer ◽

Early Detection ◽

Liquid Biopsy ◽

Residual Disease ◽

Point Of View ◽

Liquid Biopsies ◽

Cell Therapies ◽

Technological Advances ◽

Diagnostic Modalities ◽

Tumor Genome

In the field of colorectal cancer (CRC) treatment, diagnostic modalities and chemotherapy regimens have progressed remarkably in the last two decades. However, it is still difficult to identify minimal residual disease (MRD) necessary for early detection of recurrence/relapse of tumors and to select and provide appropriate drugs timely before a tumor becomes multi-drug-resistant and more aggressive. We consider the leveraging of in-depth genomic profiles of tumors as a significant breakthrough to further improve the overall prognosis of CRC patients. With the recent technological advances in methodologies and bioinformatics, the genomic profiles can be analyzed profoundly without delay by blood-based tests—‘liquid biopsies’. From a clinical point of view, a minimally-invasive liquid biopsy is thought to be a promising method and can be implemented in routine clinical settings in order to meet unmet clinical needs. In this review, we highlighted clinical usefulness of liquid biopsies in the clinical management of CRC patients, including cancer screening, detection of MRD, selection of appropriate molecular-targeted drugs, monitoring of the treatment responsiveness, and very early detection of recurrence/relapse of the disease. In addition, we addressed a possibility of adoptive T cell therapies and a future personalized immunotherapy based on tumor genome information.

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The Role of Liquid Biopsy in Early Diagnosis of Lung Cancer

Frontiers in Oncology ◽

10.3389/fonc.2021.634316 ◽

2021 ◽

Vol 11 ◽

Author(s):

Cláudia Freitas ◽

Catarina Sousa ◽

Francisco Machado ◽

Mariana Serino ◽

Vanessa Santos ◽

...

Keyword(s):

Lung Cancer ◽

Clinical Practice ◽

Early Detection ◽

Liquid Biopsy ◽

Diagnostic Tools ◽

Great Promise ◽

Liquid Biopsies ◽

Micro Rnas ◽

Potential Applicability

Liquid biopsy is an emerging technology with a potential role in the screening and early detection of lung cancer. Several liquid biopsy-derived biomarkers have been identified and are currently under ongoing investigation. In this article, we review the available data on the use of circulating biomarkers for the early detection of lung cancer, focusing on the circulating tumor cells, circulating cell-free DNA, circulating micro-RNAs, tumor-derived exosomes, and tumor-educated platelets, providing an overview of future potential applicability in the clinical practice. While several biomarkers have shown exciting results, diagnostic performance and clinical applicability is still limited. The combination of different biomarkers, as well as their combination with other diagnostic tools show great promise, although further research is still required to define and validate the role of liquid biopsies in clinical practice.

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The detection of specific hypermethylated WIF1 and NPY genes in circulating DNA by crystal digital PCR™ is a powerful new tool for colorectal cancer diagnosis and screening

BMC Cancer ◽

10.1186/s12885-021-08816-2 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Alexis Overs ◽

Mylène Flammang ◽

Eric Hervouet ◽

Laurent Bermont ◽

Jean-Luc Pretet ◽

...

Keyword(s):

Liquid Biopsy ◽

Digital Pcr ◽

Circulating Tumor Dna ◽

Point Of View ◽

University Hospital ◽

Liquid Biopsies ◽

Tissue Samples ◽

Mutation Status ◽

Tumor Tissues ◽

Tumor Stages

Abstract Background In oncology, liquid biopsy is of major relevance from theranostic point of view. The searching for mutations in circulating tumor DNA (ctDNA) in case of colorectal cancers (CRCs) allows the optimization of patient care. In this context, independent of mutation status biomarkers are required for its detection to confirm the presence of ctDNA in liquid biopsies. Indeed, the hypermethylation of NPY and WIF1 genes appear to be an ideal biomarker for the specific detection of ctDNA in CRCs. The objective of this work is to develop the research of hypermethylation of NPY and WIF1 by Crystal Digital PCR™ for the detection of ctDNA in CRCs. Methods Detection of hypermethylated NPY and WIF1 was developed on Cristal digital PCR™. Biological validation was performed from a local cohort of 22 liquid biopsies and 23 tissue samples from patients with CRC. These patients were treated at the University Hospital of Besancon (France). Results The local cohort study confirmed that NPY and WIF1 were significantly hypermethylated in tumor tissues compared to adjacent non-tumor tissues (WIF1 p < 0.001; NPY p < 0.001; non-parametric Wilcoxon paired-series test). Histological characteristics, tumor stages or mutation status were not correlated to the methylation profiles. On the other hand, hypermethylation of NPY or WIF1 in liquid biopsy had a 95.5% [95%CI 77–100%] sensitivity and 100% [95%CI 69–100%] specificity. Conclusion Using Crystal digital PCR™, this study shows that hypermethylation of NPY and WIF1 are constant specific biomarkers of CRCs regardless of a potential role in carcinogenesis.

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From Sampling to Sequencing: A Liquid Biopsy Pre-Analytic Workflow to Maximize Multi-Layer Genomic Information from a Single Tube

Cancers ◽

10.3390/cancers13123002 ◽

2021 ◽

Vol 13 (12) ◽

pp. 3002

Author(s):

Kendra K. Maass ◽

Paulina S. Schad ◽

Agnes M. E. Finster ◽

Pitithat Puranachot ◽

Fabian Rosing ◽

...

Keyword(s):

Liquid Biopsy ◽

Pcr Amplification ◽

Genomic Analysis ◽

Digital Pcr ◽

Great Promise ◽

Sample Collection ◽

Liquid Biopsies ◽

Cell Free Dna ◽

Dna And Rna ◽

Free Dna

Liquid biopsies hold great promise for the management of cancer. Reliable liquid biopsy data depend on stable and reproducible pre-analytical protocols that comply with quality measures, irrespective of the sampling and processing site. We established a workflow for plasma preservation, followed by processing, cell-free nucleic acid isolation, quantification, and enrichment of potentially tumor-derived cell-free DNA and RNA. Employing the same input material for a direct comparison of different kits and protocols allowed us to formulate unbiased recommendations for sample collection, storage, and processing. The presented workflow integrates the stabilization in Norgen, PAX, or Streck tubes and subsequent parallel isolation of cell-free DNA and RNA with NucleoSnap and NucleoSpin. Qubit, Bioanalyzer, and TapeStation quantification and quality control steps were optimized for minimal sample use and high sensitivity and reproducibility. We show the efficiency of the proposed workflow by successful droplet digital PCR amplification of both cell-free DNA and RNA and by detection of tumor-specific alterations in low-coverage whole-genome sequencing and DNA methylation profiling of plasma-derived cell-free DNA. For the first time, we demonstrated successful parallel extraction of cell-free DNA and RNA from plasma samples. This workflow paves the road towards multi-layer genomic analysis from one single liquid biopsy sample.

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Ultra-high Temperature (UHT) Processing: Technological Significance and Updates

Current Nutrition & Food Science ◽

10.2174/1573401316666200217111113 ◽

2020 ◽

Vol 16 (8) ◽

pp. 1183-1195

Author(s):

Prasad Rasane ◽

Nitya Sharma ◽

Sana Fatma ◽

Sawinder Kaur ◽

Alok Jha ◽

...

Keyword(s):

High Temperature ◽

Shelf Life ◽

Raw Milk ◽

Fundamental Principle ◽

Point Of View ◽

Cold Chain ◽

Historical Significance ◽

Perishable Commodity ◽

Quality Of Milk ◽

Ultra High Temperature

Background: Background: Milk forms an integral part of the human diet from the nutritional point of view. Besides nutrition, it has also unique functional properties which are harnessed by the industry for numerous uses. Being highly perishable specific techniques are required to minimize the losses during processing and adequate preservation of this precious commodity. In the U.S. and many other parts of the world, the traditional pasteurization of milk requires a minimum heat treatment of 72ºC for 15 seconds with subsequent refrigeration. However, the advent of Ultra High Temperature (UHT) treatment of milk has added a new dimension to the marketing of liquid milk in urban as well as remote areas without the requirement of cold chain management. The distinctive feature of UHT processed milk is that it is commercially-sterile-not pasteurized and so has long shelf life at room temperature. UHT milk, also known as long-life milk, is emerging as an attractive commercial alternative offering a hygienic product of unmatched quality, which can be bought anywhere, at any time and in any quantity. The present review will discuss numerous aspects of UHT processing of milk with reference to historical significance, fundamental principle, various systems used and prerequisites, type of exchangers used, fouling and other defects in system, chemical and microbiological effect of the treatment, its effect on nutritional components, organoleptic quality of milk and the advantage and involved challenges of the process. Conclusion: Raw milk is easily contaminated with pathogens and microbes and hence its consumption of raw milk is associated with certain ill health effects. Therefore, heating milk before consumption is strongly suggested. Thus, UHT treatment of milk is done to ensure microbial safety and also to extend the shelf life of this highly perishable commodity. Heating milk at such a high temperature is often associated with the change of organoleptic properties like change in flavor or cooked flavor, rancidity due to microbes or acid flavor, etc. But UHT treatment does not substantially decrease the nutritional value or any other benefits of milk.

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The Liquid Biopsy for Lung Cancer: State of the Art, Limitations and Future Developments

Cancers ◽

10.3390/cancers13163923 ◽

2021 ◽

Vol 13 (16) ◽

pp. 3923

Author(s):

Daniel Di Capua ◽

Dara Bracken-Clarke ◽

Karine Ronan ◽

Anne-Marie Baird ◽

Stephen Finn

Keyword(s):

Lung Cancer ◽

Lung Carcinoma ◽

Targeted Therapies ◽

Liquid Biopsy ◽

Genetic Alterations ◽

Rapid Progression ◽

Liquid Biopsies ◽

Cell Lung Carcinoma ◽

Genetic Sequencing ◽

Tissue Biopsy

Lung cancer is a leading cause of cancer-related deaths, contributing to 18.4% of cancer deaths globally. Treatment of non-small cell lung carcinoma has seen rapid progression with targeted therapies tailored to specific genetic drivers. However, identifying genetic alterations can be difficult due to lack of tissue, inaccessible tumors and the risk of complications for the patient with serial tissue sampling. The liquid biopsy provides a minimally invasive method which can obtain circulating biomarkers shed from the tumor and could be a safer alternative to tissue biopsy. While tissue biopsy remains the gold standard, liquid biopsies could be very beneficial where serial sampling is required, such as monitoring disease progression or development of resistance mutations to current targeted therapies. Liquid biopsies also have a potential role in identifying patients at risk of relapse post treatment and as a component of future lung cancer screening protocols. Rapid developments have led to multiple platforms for isolating circulating tumor cells (CTCs) and detecting circulating tumor DNA (ctDNA); however, standardization is lacking, especially in lung carcinoma. Additionally, clonal hematopoiesis of uncertain clinical significance must be taken into consideration in genetic sequencing, as it introduces the potential for false positives. Various biomarkers have been investigated in liquid biopsies; however, in this review, we will concentrate on the current use of ctDNA and CTCs, focusing on the clinical relevance, current and possible future applications and limitations of each.

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The ethics of pandemic preparedness revisited - autonomy, quarantine, transferability and trust

European Journal of Public Health ◽

10.1093/eurpub/ckaa166.182 ◽

2020 ◽

Vol 30 (Supplement_5) ◽

Author(s):

P Schröder-Bäck ◽

T Schloemer ◽

K Martakis ◽

C Brall

Keyword(s):

Crisis Management ◽

Ethical Issues ◽

Lessons Learned ◽

Point Of View ◽

Ethical Challenges ◽

Pandemic Preparedness ◽

Ethical Aspects ◽

Outbreak Management ◽

Ethics Framework ◽

Ethical Point

Abstract Background The outbreak of SARS in 2002 lead to a public health ethics discourse. The crisis management of that time was ethically analysed and lessons to be learned discussed. Scholarship and WHO, among others, developed an ethics of pandemic preparedness. The current “corona crisis” also faces us with ethical challenges. This presentation is comparing the two crises from an ethical point of view and a focus on Europe. Methods An ethics framework for pandemic preparedness (Schröder et al. 2006 and Schröder-Bäck 2014) is used to make a synopsis of ethical issues. Ethical aspects of 2002 and 2020 that were discussed in the literature and in the media are compared. For 2020, the focus is on interventions in Italy, Germany, Switzerland, and the Netherlands. Results Topics that emerged from the 2002 crisis were, among others, revolving around aspects of stigmatisation and fair distribution of scarce resources (esp. vaccines, antivirals). Currently, most urgent and ethically challenging aspects relate to social distancing vs. autonomy: Isolation and quarantine are handled differently across Europe and the EU. Questions of transferability of such interventions prevail. Contexts vary vertically over time (2002 vs. 2020) and horizontally (e.g. between Italy and Germany at the same time). Furthermore, trust in authorities, media and health information is a key issue. Conclusions Ethical aspects are key for good pandemic preparedness and management. The context of the crises between 2002 and 2020 has slightly changed, also based on “lessons learned” from 2002. This has implications on ethical issues that are being discussed. New lessons will have to be learned from the 2020 crisis. Key messages Pandemic preparedness and outbreak management entail many ethical tensions that need to be addressed. Currently, questions of trust and transferability are key to the crisis management, further ethical issues could still emerge.

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Emerging Lab-on-a-Chip Approaches for Liquid Biopsy in Lung Cancer: Status in CTCs and ctDNA Research and Clinical Validation

Cancers ◽

10.3390/cancers13092101 ◽

2021 ◽

Vol 13 (9) ◽

pp. 2101

Author(s):

Ângela Carvalho ◽

Gabriela Ferreira ◽

Duarte Seixas ◽

Catarina Guimarães-Teixeira ◽

Rui Henrique ◽

...

Keyword(s):

Lung Cancer ◽

Liquid Biopsy ◽

Residual Disease ◽

Lab On A Chip ◽

Microfluidic Devices ◽

Early Recurrence ◽

Circulating Tumor Dna ◽

Clinical Validation ◽

Liquid Biopsies ◽

Lung Cancer Patients

Despite the intensive efforts dedicated to cancer diagnosis and treatment, lung cancer (LCa) remains the leading cause of cancer-related mortality, worldwide. The poor survival rate among lung cancer patients commonly results from diagnosis at late-stage, limitations in characterizing tumor heterogeneity and the lack of non-invasive tools for detection of residual disease and early recurrence. Henceforth, research on liquid biopsies has been increasingly devoted to overcoming these major limitations and improving management of LCa patients. Liquid biopsy is an emerging field that has evolved significantly in recent years due its minimally invasive nature and potential to assess various disease biomarkers. Several strategies for characterization of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have been developed. With the aim of standardizing diagnostic and follow-up practices, microfluidic devices have been introduced to improve biomarkers isolation efficiency and specificity. Nonetheless, implementation of lab-on-a-chip platforms in clinical practice may face some challenges, considering its recent application to liquid biopsies. In this review, recent advances and strategies for the use of liquid biopsies in LCa management are discussed, focusing on high-throughput microfluidic devices applied for CTCs and ctDNA isolation and detection, current clinical validation studies and potential clinical utility.

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Platelets, immune cells and the coagulation cascade; friend or foe of the circulating tumour cell?

Molecular Cancer ◽

10.1186/s12943-021-01347-1 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Mark P. Ward ◽

Laura E. Kane ◽

Lucy A. Norris ◽

Bashir M. Mohamed ◽

Tanya Kelly ◽

...

Keyword(s):

Cancer Cells ◽

Immune Cells ◽

Immune Cell ◽

Circulatory System ◽

Morphological Characteristics ◽

Metastatic Potential ◽

Coagulation Cascade ◽

Molecular Profile ◽

Great Promise ◽

Liquid Biopsies

AbstractCancer cells that transit from primary tumours into the circulatory system are known as circulating tumour cells (CTCs). These cancer cells have unique phenotypic and genotypic characteristics which allow them to survive within the circulation, subsequently extravasate and metastasise. CTCs have emerged as a useful diagnostic tool using “liquid biopsies” to report on the metastatic potential of cancers. However, CTCs by their nature interact with components of the blood circulatory system on a constant basis, influencing both their physical and morphological characteristics as well as metastatic capabilities. These properties and the associated molecular profile may provide critical diagnostic and prognostic capabilities in the clinic. Platelets interact with CTCs within minutes of their dissemination and are crucial in the formation of the initial metastatic niche. Platelets and coagulation proteins also alter the fate of a CTC by influencing EMT, promoting pro-survival signalling and aiding in evading immune cell destruction. CTCs have the capacity to directly hijack immune cells and utilise them to aid in CTC metastatic seeding processes. The disruption of CTC clusters may also offer a strategy for the treatment of advance staged cancers. Therapeutic disruption of these heterotypical interactions as well as direct CTC targeting hold great promise, especially with the advent of new immunotherapies and personalised medicines. Understanding the molecular role that platelets, immune cells and the coagulation cascade play in CTC biology will allow us to identify and characterise the most clinically relevant CTCs from patients. This will subsequently advance the clinical utility of CTCs in cancer diagnosis/prognosis.

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