Advances in liquid biopsy on-chip for cancer management: Technologies, biomarkers, and clinical analysis

Circulating Tumor cells and multiple indicators combined to identify the risk of poorer prognosis in patients with resected non-small cell lung cancer

BACKGROUND

Surgical resection is an important treatment option for patients with non-small cell lung cancer (NSCLC). However, recurrence and survival rates remain a cause of concern. To further improve prognosis, more studies have focused on liquid biopsy, which has significant value as a prognostic factor for defining the risk stratification of postoperative NSCLC patients. This study aimed to identify circulating tumor cells (CTCs) as biomarkers that indicate a poor prognosis, combined with multiple indicators to determine prognostic risks in advance and develop individualized treatment strategies.

METHODS

Between November 2015 and August 2018, 65 radical resected patients with NSCLC were analyzed. Preoperative CTCs were collected, and follow-up lasted until August 2023. Overall survival (OS) and disease-free survival (DFS) were the primary outcomes.

RESULTS

With an 11 CTC unit threshold, the high preoperative CTC level group had worse OS and DFS than the low-level group, suggesting that preoperative CTC levels have prognostic value. Time-dependent receiver operating characteristic (ROC) curves also showed satisfactory predictive efficiency of CTCs. Univariate analysis revealed that preoperative CTC levels were significantly associated with increasing risks for OS and DFS. Moreover, we combined CTCs and multiple indicators to provide a reference for a group at high risk of adverse outcomes.

CONCLUSIONS

CTCs serve as feasible biomarkers for predicting postoperative prognosis in NSCLC patients. The combination of hematological, radiological, and pathological features could be valuable tools to guide postoperative management and treatment decisions in these patients. A multimodal prognostic approach is important for the clinical evaluation of lung cancer.

DNA/RNA-based electrochemical nanobiosensors for early detection of cancers

Nucleic acids, like DNA and RNA, serve as versatile recognition elements in electrochemical biosensors, demonstrating notable efficacy in detecting various cancer biomarkers with high sensitivity and selectivity. These biosensors offer advantages such as cost-effectiveness, rapid response, ease of operation, and minimal sample preparation. This review provides a comprehensive overview of recent developments in nucleic acid-based electrochemical biosensors for cancer diagnosis, comparing them with antibody-based counterparts. Specific examples targeting key cancer biomarkers, including prostate-specific antigen, microRNA-21, and carcinoembryonic antigen, are highlighted. The discussion delves into challenges and limitations, encompassing stability, reproducibility, interference, and standardization issues. The review suggests future research directions, exploring new nucleic acid recognition elements, innovative transducer materials and designs, novel signal amplification strategies, and integration with microfluidic devices or portable instruments. Evaluating these biosensors in clinical settings using actual samples from cancer patients or healthy donors is emphasized. These sensors are sensitive and specific at detecting non-communicable and communicable disease biomarkers. DNA and RNA's self-assembly, programmability, catalytic activity, and dynamic behavior enable adaptable sensing platforms. They can increase biosensor biocompatibility, stability, signal transduction, and amplification with nanomaterials. In conclusion, nucleic acids-based electrochemical biosensors hold significant potential to enhance cancer detection and treatment through early and accurate diagnosis.

Optimization of Surface Functionalizations for Ring Resonator-Based Biosensors

Liquid biopsy is expected to become widespread in the coming years thanks to point of care devices, which can include label-free biosensors. The surface functionalization of biosensors is a crucial aspect that influences their overall performance, resulting in the accurate, sensitive, and specific detection of target molecules. Here, the surface of a microring resonator (MRR)-based biosensor was functionalized for the detection of protein biomarkers. Among the several existing functionalization methods, a strategy based on aptamers and mercaptosilanes was selected as the most highly performing approach. All steps of the functionalization protocol were carefully characterized and optimized to obtain a suitable protocol to be transferred to the final biosensor. The functionalization protocol comprised a preliminary plasma treatment aimed at cleaning and activating the surface for the subsequent silanization step. Different plasma treatments as well as different silanes were tested in order to covalently bind aptamers specific to different biomarker targets, i.e., C-reactive protein, SARS-CoV-2 spike protein, and thrombin. Argon plasma and 1% v/v mercaptosilane were found as the most suitable for obtaining a homogeneous layer apt to aptamer conjugation. The aptamer concentration and time for immobilization were optimized, resulting in 1 µM and 3 h, respectively. A final passivation step based on mercaptohexanol was also implemented. The functionalization protocol was then evaluated for the detection of thrombin with a photonic biosensor based on microring resonators. The preliminary results identified the successful recognition of the correct target as well as some limitations of the developed protocol in real measurement conditions.

Liquid biopsy for precision diagnostics and therapeutics

Liquid biopsy (LB) has emerged as a highly promising and non-invasive diagnostic approach, particularly in the field of oncology, and has garnered interest in various medical disciplines. This technique involves the examination of biomolecules released into physiological fluids, such as urine samples, blood, and cerebrospinal fluid (CSF). The analysed biomolecules included circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), cell-free DNA (cfDNA), exosomes, and other cell-free components. In contrast to conventional tissue biopsies, LB provides minimally invasive diagnostics, offering invaluable insights into tumor characteristics, treatment response, and early disease detection. This Review explores the contemporary landscape of technologies and clinical applications in the realm of LB, with a particular emphasis on the isolation and analysis of ctDNA and/or cfDNA. Various methodologies have been employed, including droplet digital polymerase chain reaction (DDP), BEAMing (beads, emulsion, amplification, and magnetics), TAm-Seq (tagged-amplicon deep sequencing), CAPP-Seq (cancer personalized profiling by deep sequencing), WGBS-Seq (whole genome bisulfite sequencing), WES (whole exome sequencing), and WGS (whole-genome sequencing). Additionally, CTCs have been successfully isolated through biomarker-based cell capture, employing both positive and negative enrichment strategies based on diverse biophysical and other inherent properties. This approach also addresses challenges and limitations associated with liquid biopsy techniques, such as sensitivity, specificity, standardization and interpretability of findings. This review seeks to identify the current technologies used in liquid biopsy samples, emphasizing their significance in identifying tumor markers for cancer detection, prognosis, and treatment outcome monitoring.

Increased Plasmatic Levels of Exosomes Are Significantly Related to Relapse Rate in Patients with Oral Squamous Cell Carcinoma: A Cohort Study

BACKGROUND

Oral squamous cell carcinoma (OSCC) is characterized by an immunosuppressive tumor microenvironment. Their plasma-derived exosomes deliver immunomodulatory molecules and cargo that correlate significantly with clinical parameters. This study aims to assess the exosomal profile as a potential tool for early detection of relapse and long-term outcomes in OSCC patients undergoing conventional therapy.

METHODS

27 OSCC patients with a median 38-month follow-up were included in this study. The relationship between NTA-derived parameters and clinical pathological parameters was examined, and receiver operating characteristic (ROC) curves were utilized to evaluate the diagnostic efficacy of these values in detecting cancer relapse.

RESULTS

Plasmatic levels of exosomes prior to surgery showed a drastic reduction after surgical intervention (8.08E vs. 1.41 × 109 particles/mL, p = 0.006). Postsurgical concentrations of exosomes were higher in patients who experienced relapse compared to those who remained disease-free (2.97 × 109 vs. 1.11 × 109 particles/mL, p = 0.046). Additionally, patients who relapsed exhibited larger exosome sizes after surgery (141.47 vs. 132.31 nm, p = 0.03). Patients with lower concentrations of exosomes prior to surgery demonstrated better disease-free survival compared to those with higher levels (p = 0.012). ROC analysis revealed an area under the curve of 0.82 for presurgical exosome concentration in identifying relapse.

CONCLUSIONS

Presurgical exosomal plasmatic levels serve as independent predictors of early recurrence and survival in OSCC. All in all, our findings indicate that the detection of peripheral exosomes represents a novel tool for the clinical management of OSCC, with potential implications for prognosis assessment.

Assessment and prediction of glioblastoma therapy response: challenges and opportunities

Glioblastoma is the most aggressive type of primary adult brain tumour. The median survival of patients with glioblastoma remains approximately 15 months, and the 5-year survival rate is <10%. Current treatment options are limited, and the standard of care has remained relatively constant since 2011. Over the last decade, a range of different treatment regimens have been investigated with very limited success. Tumour recurrence is almost inevitable with the current treatment strategies, as glioblastoma tumours are highly heterogeneous and invasive. Additionally, another challenging issue facing patients with glioblastoma is how to distinguish between tumour progression and treatment effects, especially when relying on routine diagnostic imaging techniques in the clinic. The specificity of routine imaging for identifying tumour progression early or in a timely manner is poor due to the appearance similarity of post-treatment effects. Here, we concisely describe the current status and challenges in the assessment and early prediction of therapy response and the early detection of tumour progression or recurrence. We also summarize and discuss studies of advanced approaches such as quantitative imaging, liquid biomarker discovery and machine intelligence that hold exceptional potential to aid in the therapy monitoring of this malignancy and early prediction of therapy response, which may decisively transform the conventional detection methods in the era of precision medicine.

Peripheral Blood Mononuclear Cell derived Biomarker detection using eXplainable Artificial Intelligence (XAI) provides better diagnosis of Breast Cancer

The incidence and mortality rate of breast cancer increases yearly by an average of 1.44 % and 0.23 %, respectively. Till 2021, there were 7.8 million women who had been diagnosed with breast cancer within 5 years. Biopsies of tumors are often expensive and invasive and raise the risk of serious complications like infection, excessive bleeding, and puncture damage to nearby tissues and organs. Early detection biomarkers are often variably expressed in different patients and may even be below the detection level at an early stage. Hence PBMC that shows alteration in gene profile as a result of interaction with tumor antigens may serve as a better early detection biomarker. Also, such alterations in immune gene profile in PBMCs are more prone to detection despite variability in different breast cancer mutants.This study aimed to identify potential diagnostic biomarkers for breast cancer using eXplainable Artificial Intelligence (XAI) on XGBoost machine learning (ML) models trained on a binary classification dataset containing the expression data of PBMCs from 252 breast cancer patients and 194 healthy women.After effectively adding SHAP values further into the XGBoost model, ten important genes related to breast cancer development were discovered to be effective potential biomarkers. Our studies showed that SVIP, BEND3, MDGA2, LEF1-AS1, PRM1, TEX14, MZB1, TMIGD2, KIT, and FKBP7 are key genes that impact model prediction. These genes may serve as early, non-invasive diagnostic and prognostic biomarkers for breast cancer patients.

SARS-CoV-2-on-Chip for Long COVID Management

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a "wicked evil" in this century due to its extended progression and huge human mortalities. Although the diagnosis of SARS-CoV-2 viral infection is made simple and practical by employing reverse transcription polymerase chain reaction (RT-PCR) investigation, the process is costly, complex, time-consuming, and requires experts for testing and the constraints of a laboratory. Therefore, these challenges have raised the paradigm of on-site portable biosensors on a single chip, which reduces human resources and enables remote access to minimize the overwhelming burden on the existing global healthcare sector. This article reviews the recent advancements in biosensors for long coronavirus disease (COVID) management using a multitude of devices, such as point-of-care biosensors and lab-on-chip biosensors. Furthermore, it details the shift in the paradigm of SARS-CoV-2-on-chip biosensors from the laboratory to on-site detection with intelligent and economical operation, representing near-future diagnostic technologies for public health emergency management.

Identification of Metastasis-Associated Genes in Cutaneous Squamous Cell Carcinoma Based on Bioinformatics Analysis and Experimental Validation

INTRODUCTION

Cutaneous squamous cell carcinoma (cSCC) is a global malignant tumor with a high degree of malignancy. Once metastasis occurs, it will lead to poor prognosis and even death. This study attempts to find out the central genes closely related to cSCC metastasis, so as to clarify the molecular regulatory mechanism of cSCC metastasis and open up new ideas for clinical treatment.

METHODS

Firstly, cSCC data set GSE98767 was used to establish a tumor metastasis model via clustering analysis. The key module and hub genes associated with cSCC metastasis were analyzed by weighted gene co-expression analysis (WGCNA). Next, the prognostic functions of hub genes were identified by functional and pathway enrichment analysis, pan-cancer analysis, and receiver operating characteristic-area under the curve (ROC-AUC) validation. Finally, the key genes were verified by clinical sample detection and biological in vitro test.

RESULTS

A total of 19 hub genes related to cSCC metastasis were identified. They were highly expressed in cSCC metastatic tissues and were mainly enriched in cellular material and energy metabolism pathways. Overall survival (OS) and disease-free survival (DFS) results from pan-cancer analysis showed that eight and six highly expressed genes, respectively, with PAPSS2 and SCG5 had highly reliable ROC-AUC validation values and were poor prognostic factors. Clinical and biological tests also confirmed the upregulation of PAPSS2 and SCG5 in cSCC. Deletion of PAPSS2 and SCG5 resulted in decreased viability, migration, and invasion of A-431 cells.

CONCLUSION

PAPSS2 and SCG5 may be important factors for cSCC metastasis, and they are involved in the regulation of cSCC cell viability, migration, and invasion.

Liquid Biopsy and Circulating Biomarkers for the Diagnosis of Precancerous and Cancerous Oral Lesions

Oral cancer is one of the most common malignancies worldwide, accounting for 2% of all cases annually and 1.8% of all cancer deaths. To date, tissue biopsy and histopathological analyses are the gold standard methods for the diagnosis of oral cancers. However, oral cancer is generally diagnosed at advanced stages with a consequent poor 5-year survival (~50%) due to limited screening programs and inefficient physical examination strategies. To address these limitations, liquid biopsy is recently emerging as a novel minimally invasive tool for the early identification of tumors as well as for the evaluation of tumor heterogeneity and prognosis of patients. Several studies have demonstrated that liquid biopsy in oral cancer could be useful for the detection of circulating biomarkers including circulating tumor DNA (ctDNA), microRNAs (miRNAs), proteins, and exosomes, thus improving diagnostic strategies and paving the way to personalized medicine. However, the application of liquid biopsy in oral cancer is still limited and further studies are needed to better clarify its clinical impact. The present manuscript aims to provide an updated overview of the potential use of liquid biopsy as an additional tool for the management of oral lesions by describing the available methodologies and the most promising biomarkers.

Current Status, Opportunities, and Challenges of Exosomes in Oral Cancer Diagnosis and Treatment

Oral cancer is one of the most common cancers in the world, with more than 300,000 cases diagnosed each year, of which oral squamous cell carcinoma accounts for more than 90%, with a 5-year survival rate of only 40–60%, and poor prognosis. Exploring new strategies for the early diagnosis and treatment of oral cancer is key to improving the survival rate. Exosomes are nanoscale lipid bilayer membrane vesicles that are secreted by almost all cell types. During the development of oral cancer, exosomes can transport their contents (DNA, RNA, proteins, etc) to target cells and promote or inhibit the proliferation, invasion, and metastasis of oral cancer cells by influencing the host immune response, drug-resistant metastasis, and tumour angiogenesis. Therefore, exosomes have great potential and advantages as biomarkers for oral cancer diagnosis, and as drug delivery vehicles or targets for oral cancer therapy. In this review, we first describe the biogenesis, biological functions, and isolation methods of exosomes, followed by their relationship with oral cancer. Here, we focused on the potential of exosomes as oral cancer biomarkers, drug carriers, and therapeutic targets. Finally, we provide an insightful discussion of the opportunities and challenges of exosome application in oral cancer diagnosis and treatment, intending to offer new ideas for the clinical management of oral cancer.

Systematic Review of Epigenetic Therapies for Treatment of IDH-mutant Glioma

BACKGROUND

Isocitrate dehydrogenase (IDH) mutations are present in 70% of World Health Organization grade II and III gliomas. IDH mutation induces accumulation of the oncometabolite 2-hydroxyglutarate. Therefore, therapies targeting reversal of epigenetic dysregulation in gliomas have been suggested. However, the utility of epigenetic treatments in gliomas remains unclear. Here, we present the first clinical systematic review of epigenetic therapies in treatment of IDH-mutant gliomas and highlight their safety and efficacy.

METHODS

We conducted a systematic search of electronic databases from 2000 to January 2021 following PRISMA guidelines. Articles were screened to include clinical usage of epigenetic therapies in case reports, prospective case series, or clinical trials. Primary and secondary outcomes included safety/tolerability of epigenetic therapies and progression-free survival/overall survival, respectively.

RESULTS

A total of 133 patients across 8 clinical studies were included in our analysis. IDH inhibitors appear to have the best safety profile, with an overall grade 3/grade 4 adverse event rate of 9%. Response rates to IDH-mutant inhibitors were highest in nonenhancing gliomas (stable disease achieved in 55% of patients). In contrast, histone deacetylase inhibitors demonstrate a lower safety profile with single-study adverse events as high as 28%.

CONCLUSION

IDH inhibitors appear promising given their benign toxicity profile and ease of monitoring. Histone deacetylase inhibitors appear to have a narrow therapeutic index, as lower concentrations do not appear effective, while increased doses can produce severe immunosuppressive effects. Preliminary data suggest that epigenetic therapies are generally well tolerated and may control disease in certain patient groups, such as those with nonenhancing lesions.

Artificial Intelligence and Circulating Cell-Free DNA Methylation Profiling: Mechanism and Detection of Alzheimer's Disease

Background: Despite extensive efforts, significant gaps remain in our understanding of Alzheimer’s disease (AD) pathophysiology. Novel approaches using circulating cell-free DNA (cfDNA) have the potential to revolutionize our understanding of neurodegenerative disorders. Methods: We performed DNA methylation profiling of cfDNA from AD patients and compared them to cognitively normal controls. Six Artificial Intelligence (AI) platforms were utilized for the diagnosis of AD while enrichment analysis was used to elucidate the pathogenesis of AD. Results: A total of 3684 CpGs were significantly (adj. p-value < 0.05) differentially methylated in AD versus controls. All six AI algorithms achieved high predictive accuracy (AUC = 0.949−0.998) in an independent test group. As an example, Deep Learning (DL) achieved an AUC (95% CI) = 0.99 (0.95−1.0), with 94.5% sensitivity and specificity. Conclusion: We describe numerous epigenetically altered genes which were previously reported to be differentially expressed in the brain of AD sufferers. Genes identified by AI to be the best predictors of AD were either known to be expressed in the brain or have been previously linked to AD. We highlight enrichment in the Calcium signaling pathway, Glutamatergic synapse, Hedgehog signaling pathway, Axon guidance and Olfactory transduction in AD sufferers. To the best of our knowledge, this is the first reported genome-wide DNA methylation study using cfDNA to detect AD.

Microfluidic-Based Technologies for CTC Isolation: A Review of 10 Years of Intense Efforts towards Liquid Biopsy

The selection of circulating tumor cells (CTCs) directly from blood as a real-time liquid biopsy has received increasing attention over the past ten years, and further analysis of these cells may greatly aid in both research and clinical applications. CTC analysis could advance understandings of metastatic cascade, tumor evolution, and patient heterogeneity, as well as drug resistance. Until now, the rarity and heterogeneity of CTCs have been technical challenges to their wider use in clinical studies, but microfluidic-based isolation technologies have emerged as promising tools to address these limitations. This review provides a detailed overview of latest and leading microfluidic devices implemented for CTC isolation. In particular, this study details must-have device performances and highlights the tradeoff between recovery and purity. Finally, the review gives a report of CTC potential clinical applications that can be conducted after CTC isolation. Widespread microfluidic devices, which aim to support liquid-biopsy-based applications, will represent a paradigm shift for cancer clinical care in the near future.

Microfluidic Approaches and Methods Enabling Extracellular Vesicle Isolation for Cancer Diagnostics

Advances in cancer research over the past half-century have clearly determined the molecular origins of the disease. Central to the use of molecular signatures for continued progress, including rapid, reliable, and early diagnosis is the use of biomarkers. Specifically, extracellular vesicles as biomarker cargo holders have generated significant interest. However, the isolation, purification, and subsequent analysis of these extracellular vesicles remain a challenge. Technological advances driven by microfluidics-enabled devices have made the challenges for isolation of extracellular vesicles an emerging area of research with significant possibilities for use in clinical settings enabling point-of-care diagnostics for cancer. In this article, we present a tutorial review of the existing microfluidic technologies for cancer diagnostics with a focus on extracellular vesicle isolation methods.

Plasmonic Nanoparticle Conjugation for Nucleic Acid Biosensing

This chapter details the use of gold nanorods conjugated with peptide nucleic acid probes for sequence-specific detection of circulating tumor DNA (ctDNA). ctDNA is gaining increased attention as a biomarker for liquid biopsy, the process of detecting molecules in the peripheral blood rather than a tissue sample. It has wide ranging applications as a diagnostic and prognostic biomarker with a similar mutational profile as the tumor. Plasmonic nanoparticles offer a relatively rapid, amplification-free method for detection of ctDNA through the use of sequence-specific peptide nucleic acid (PNA) probes. In this chapter, we discuss methods for probe design, conjugation to plasmonic particles, and ctDNA quantitation with the resulting sensor. This chapter is a resource for those looking to use plasmonic gold particles for sensing in a solution format for a range of applications.

Exosomes as Powerful Engines in Cancer: Isolation, Characterization and Detection Techniques

Exosomes, powerful extracellular nanovesicles released from almost all types of living cells, are considered the communication engines (messengers) that control and reprogram physiological pathways inside target cells within a community or between different communities. The cell-like structure of these extracellular vesicles provides a protective environment for their proteins and DNA/RNA cargos, which serve as biomarkers for many malicious diseases, including infectious diseases and cancers. Cancer-derived exosomes control cancer metastasis, prognosis, and development. In addition to the unique structure of exosomes, their nanometer size and tendency of interacting with cells makes them a viable novel drug delivery solution. In recent years, numerous research efforts have been made to quantify and characterize disease-derived exosomes for diagnosis, monitoring, and therapeutic purposes. This review aims to (1) relate exosome biomarkers to their origins, (2) focus on current isolation and detection methods, (3) discuss and evaluate the proposed technologies deriving from exosome research for cancer treatment, and (4) form a conclusion about the prospects of the current exosome research.

The scope of liquid biopsy in the clinical management of oral cancer

Oral squamous cell carcinoma (OSCC) is one of the most prevalent forms of head and neck cancer, and it remains a leading cause of death in developing countries. Failure to detect the disease at an early stage is the main reason for the lack of improvement in the overall survival rate over the decades. Even though tissue biopsy is considered as the gold standard for diagnosis and molecular workup, it is an invasive, expensive and time-consuming procedure. Besides, it may not indicate the genetic status of the entire tumour owing to the heterogeneity of the cancer. In this context, liquid biopsy could be quite useful as it provides a more representative picture of the circulating tumour cells, circulating tumour DNA, circulating RNA, and tumour-derived exosomes obtained from all types of body fluids. This technique provides real-time assessment of variations in the molecular profile of the whole tumour and enables the serial monitoring of the disease status. The method has many advantages, such as easy accessibility, reliability, reproducibility and the possibility for early detection of the disease. However, the concept is still in its infancy, and the research on its application in various tumours including OSCC is rapidly progressing.

Pushing the detection limits: strategies towards highly sensitive optical-based protein detection

Proteins are one of the main constituents of living cells. Studying the quantities of proteins under physiological and pathological conditions can give valuable insights into health status, since proteins are the functional molecules of life. To be able to detect and quantify low-abundance proteins in biofluids for applications such as early disease diagnostics, sensitive analytical techniques are desired. An example of this application is using proteins as biomarkers for detecting cancer or neurological diseases, which can provide early, lifesaving diagnoses. However, conventional methods for protein detection such as ELISA, mass spectrometry, and western blotting cannot offer enough sensitivity for certain applications. Recent advances in optical-based micro- and nano-biosensors have demonstrated promising results to detect proteins at low quantities down to the single-molecule level, shining lights on their capacities for ultrasensitive disease diagnosis and rare protein detection. However, to date, there is a lack of review articles synthesizing and comparing various optical micro- and nano-sensing methods of enhancing the limits of detections of the antibody-based protein assays. The purpose of this article is to critically review different strategies of improving assay sensitivity using miniaturized biosensors, such as assay miniaturization, improving antibody binding capacity, sample purification, and signal amplification. The pros and cons of different methods are compared, and the future perspectives of this research field are discussed.

CRISPR-Cas13 System as a Promising and Versatile Tool for Cancer Diagnosis, Therapy, and Research

Over the past decades, significant progress has been made in targeted cancer therapy. In precision oncology, molecular profiling of cancer patients enables the use of targeted cancer therapeutics. However, current diagnostic methods for molecular analysis of cancer are costly and require sophisticated equipment. Moreover, targeted cancer therapeutics such as monoclonal antibodies and small-molecule drugs may cause off-target effects and they are available for only a minority of cancer driver proteins. Therefore, there is still a need for versatile, efficient, and precise tools for cancer diagnostics and targeted cancer treatment. In recent years, the CRISPR-based genome and transcriptome engineering toolbox has expanded rapidly. Particularly, the RNA-targeting CRISPR-Cas13 system has unique biochemical properties, making Cas13 a promising tool for cancer diagnosis, therapy, and research. Cas13-based diagnostic methods allow early detection and monitoring of cancer markers from liquid biopsy samples without the need for complex instrumentation. In addition, Cas13 can be used for targeted cancer therapy through degrading and manipulating cancer-associated transcripts with high efficiency and specificity. Moreover, Cas13-mediated programmable RNA manipulation tools offer invaluable opportunities for cancer research, identification of drug-resistance mechanisms, and discovery of novel therapeutic targets. Here, we review and discuss the current use and potential applications of the CRISPR-Cas13 system in cancer diagnosis, therapy, and research. Thus, researchers will gain a deep understanding of CRISPR-Cas13 technologies, which have the potential to be used as next-generation cancer diagnostics and therapeutics.

Liquid biomarkers for the management of paediatric neuroblastoma: an approach to personalised and targeted cancer therapy

Background:

Neuroblastoma is the most common extracranial solid tumour of infancy and accounts for about 6–10% of paediatric cancers. It has a biologically and clinically heterogeneous behaviour that ranges from spontaneous regression to cases of highly aggressive metastatic disease that could be unresponsive to standard therapy. In recent years, there have been several investigations into the development of various diagnostic, predictive and prognostic biomarkers towards personalised and targeted management of the disease.

Materials and Methods:

This paper reports on the review of current clinical and emerging biomarkers used in risk assessment, screening for early detection and diagnosis, prognostication and monitoring of the response of treatment of neuroblastoma in paediatric patients.

Conclusions:

Tumour markers can significantly improve diagnosis; however, the invasive, unpleasant and inconvenient nature of current tissue biopsies limits their applications, especially in paediatric patients. Therefore, the development of a non-invasive, reliable high accurate and personalised diagnostic tool capable of early detection and rapid response is the most promising step towards advanced cancer management from tumour diagnosis, therapy to patient monitoring and represents an important step towards the promise of precision, personalised and targeted medicine. Liquid biopsy assay with wide ranges of clinical applications is emerging to hold incredible potential for advancing cancer treatment and has greater promise for diagnostic purposes, identification and tracking of tumour-specific alterations during the course of the disease and to guide therapeutic decisions.

Updates on Clinical Use of Liquid Biopsy in Colorectal Cancer Screening, Diagnosis, Follow-Up, and Treatment Guidance

Colorectal cancer (CRC) is one of the most common cancers worldwide, being the third most diagnosed in the world and the second deadliest. Solid biopsy provides an essential guide for the clinical management of patients with colorectal cancer; however, this method presents several limitations, in particular invasiveness, and cannot be used repeatedly. Recently, clinical research directed toward the use of liquid biopsy, as an alternative tool to solid biopsy, showed significant promise in several CRC clinical applications, as (1) detect CRC patients at early stage, (2) make treatment decision, (3) monitor treatment response, (4) predict relapses and metastases, (5) unravel tumor heterogeneity, and (6) detect minimal residual disease. The purpose of this short review is to describe the concept, the characteristics, the genetic components, and the technologies used in liquid biopsy in the context of the management of colorectal cancer, and finally we reviewed gene alterations, recently described in the literature, as promising potential biomarkers that may be specifically used in liquid biopsy tests.

Point-of-care cancer diagnostic devices: From academic research to clinical translation

Early and timely diagnosis of cancer plays a decisive role in appropriate treatment and improves clinical outcomes, improving public health. Significant advances in biosensor technologies are leading to the development of point-of-care (POC) diagnostics, making the testing process faster, easier, cost-effective, and suitable for on-site measurements. Moreover, the incorporation of various nanomaterials into the sensing platforms has yielded POC testing (POCT) platforms with enhanced sensitivity, cost-effectiveness and simplified detection schemes. POC cancer diagnostic devices provide promising platforms for cancer biomarker detection as compared to conventional in vitro diagnostics, which are time-consuming and require sophisticated instrumentation, centralized laboratories, and experienced operators. Current innovative approaches in POC technologies, including biosensors, smartphone interfaces, and lab-on-a-chip (LOC) devices are expected to quickly transform the healthcare landscape. However, only a few cancer POC devices (e.g. lateral flow platforms) have been translated from research laboratories to clinical care, likely due to challenges include sampling procedures, low levels of sensitivity and specificity in clinical samples, system integration and signal readout requirements. In this review, we emphasize recent advances in POC diagnostic devices for cancer biomarker detection and discuss the critical challenges which must be surmounted to facilitate their translation into clinical settings.

Electrochemical Detection and Point-of-Care Testing for Circulating Tumor Cells: Current Techniques and Future Potentials

Circulating tumor cells (CTCs) are tumor cells that escaped from the primary tumor or the metastasis into the blood and they play a major role in the initiation of metastasis and tumor recurrence. Thus, it is widely accepted that CTC is the main target of liquid biopsy. In the past few decades, the separation of CTC based on the electrochemical method has attracted widespread attention due to its convenience, rapidness, low cost, high sensitivity, and no need for complex instruments and equipment. At present, CTC detection is not widely used in the clinic due to various reasons. Point-of-care CTC detection provides us with a possibility, which is sensitive, fast, cheap, and easy to operate. More importantly, the testing instrument is small and portable, and the testing does not require specialized laboratories and specialized clinical examiners. In this review, we summarized the latest developments in the electrochemical-based CTC detection and point-of-care CTC detection, and discussed the challenges and possible trends.

Scalable Signature-Based Molecular Diagnostics Through On-chip Biomarker Profiling Coupled with Machine Learning

Molecular diagnostics have traditionally relied on discrete biological substances as diagnostic markers. In recent years however, advances in on-chip biomarker screening technologies and data analytics have enabled signature-based diagnostics. Such diagnostics aim to utilize unique combinations of multiple biomarkers or diagnostic 'fingerprints' rather than discrete analyte measurements. This approach has shown to improve both diagnostic accuracy and diagnostic specificity. In this review, signature-based diagnostics enabled by microfluidic and micro-/nano- technologies will be reviewed with a focus on device design and data analysis pipelines and methodologies. With increasing amounts of data available from microfluidic biomarker screening, isolation, and detection platforms, advanced data handling and analytics approaches can be employed. Thus, current data analysis approaches including machine learning and recent advances with image processing, along with potential future directions will be explored. Lastly, the needs and gaps in current literature will be elucidated to inform future efforts towards development of molecular diagnostics and biomarker screening technologies.

Liquid Biopsy is Instrumental for 3PM Dimensional Solutions in Cancer Management

One in every four deaths is due to cancer in Europe. In view of its increasing incidence, cancer became the leading cause of death and disease burden in Denmark, France, the Netherlands, and the UK. Without essential improvements in cancer prevention, an additional 775,000 cases of annual incidence have been prognosed until 2040. Between 1995 and 2018, the direct costs of cancer doubled from EUR 52 billion to EUR 103 billion in Europe, and per capita health spending on cancer increased by 86% from EUR 105 to EUR 195 in general, whereby Austria, Germany, Switzerland, Benelux, and France spend the most on cancer care compared to other European countries. In view of the consequent severe socio-economic burden on society, the paradigm change from a reactive to a predictive, preventive, and personalized medical approach in the overall cancer management is essential. Concepts of predictive, preventive, and personalized medicine (3PM) demonstrate a great potential to revise the above presented trends and to implement cost-effective healthcare that benefits the patient and society as a whole. At any stage, application of early and predictive diagnostics, targeted prevention, and personalization of medical services are basic pillars making 3PM particularly attractive for the patients as well as ethical and cost-effective healthcare. Optimal 3PM approach requires novel instruments such as well-designed liquid biopsy application. This review article highlights current achievements and details liquid biopsy approaches specifically in cancer management. 3PM-relevant expert recommendations are provided.

Scalable COVID-19 Detection Enabled by Lab-on-Chip Biosensors

Introduction

The emergence of a novel coronavirus, SARS-CoV-2, has highlighted the need for rapid, accurate, and point-of-care diagnostic testing. As of now, there is not enough testing capacity in the world to meet the stated testing targets, which are expected to skyrocket globally for broader testing during reopening

Aim

This review focuses on the development of lab-on-chip biosensing platforms for diagnosis of COVID-19 infection.

Results

We discuss advantages of utilizing lab-on-chip technologies in response to the current global pandemic, including their potential for low-cost, rapid sample-to-answer processing times, and ease of integration into a range of healthcare settings. We then highlight the development of magnetic, colorimetric, plasmonic, electrical, and lateral flow-based lab-on-chip technologies for the detection of SARS-CoV-2, in addition to other viruses. We focus on rapid, point-of-care technologies that can be deployed at scale, as such devices could be promising alternatives to the current gold standard of reverse transcription-polymerase chain reaction (RT-PCR) diagnostic testing.

Conclusion

This review is intended to provide an overview of the current state-of-the-field and serve as a resource for innovative development of new lab-on-chip assays for COVID-19 detection.

Role of exosomes and exosomal microRNAs in cancer

A growing body of evidence indicates that exosomes play a critical role in the cell-cell communication process. Exosomes are biological nanoparticles with an average diameter of 30-100 nm in size and are produced by almost all cell types in the human body; however, cancer cells contain higher concentrations of exosomes than healthy cells. They are released into all body fluids and contain double-stranded DNA (originated from nucleus and mitochondria), a variety of RNA species, and specific protein biomarkers that can be utilized as cancer biomarkers and therapeutic targets, and lipids. Therefore, the specific exosomes secreted by tumor cells could be used to predict the existence of the presence of a tumor in cancer patients. This review summarizes the role of exosomes in cancer development and their potential utility in the clinic.

High-Performance Nucleic Acid Sensors for Liquid Biopsy Applications

Circulating tumour nucleic acids (ctNAs) are released from tumours cells and can be detected in blood samples, providing a way to track tumors without requiring a tissue sample. This "liquid biopsy" approach has the potential to replace invasive, painful, and costly tissue biopsies in cancer diagnosis and management. However, a very sensitive and specific approach is required to detect relatively low amounts of mutant sequences linked to cancer because they are masked by the high levels of wild-type sequences. This review discusses high-performance nucleic acid biosensors for ctNA analysis in patient samples. We compare sequencing- and amplification-based methods to next-generation sensors for ctDNA and ctRNA (including microRNA) profiling, such as electrochemical methods, surface plasmon resonance, Raman spectroscopy, and microfluidics and dielectrophoresis-based assays. We present an overview of the analytical sensitivity and accuracy of these methods as well as the biological and technical challenges they present.

Effect of electrode configuration on the sensitivity of nucleic acid detection in a non-planar, flow-through, porous interdigitated electrode

Electrical impedance spectroscopy (EIS) sensors, though rapid and cost-effective, often suffer from poor sensitivity. EIS sensors modified with carbon-based transducers show a higher conductance, thereby increasing the sensitivity of the sensor toward biomolecules such as DNA. However, the EIS spectra are compromised by the parasitic capacitance of the electric double layer (EDL). Here, a new shear-enhanced, flow-through nonporous, nonplanar interdigitated microelectrode sensor has been fabricated that shifts the EDL capacitor to high frequencies. Enhanced convective transport in this sensor disrupts the diffusion dynamics of the EDL, shifting its EIS spectra to high frequency. Concomitantly, the DNA detection signal shifts to high frequency, making the sensor very sensitive and rapid with a high signal to noise ratio. The device consists of a microfluidic channel sandwiched between two sets of top and bottom interdigitated microelectrodes. One of the sets of microelectrodes is packed with carbon-based transducer material such as carboxylated single-walled carbon nanotube (SWCNT). Multiple parametric studies of three different electrode configurations of the sensor along with different carbon-based transducer materials are undertaken to understand the fundamental physics and electrochemistry. Sensors packed with SWCNT show femtomolar detection sensitivity from all the different electrode configurations for a short target-DNA. A 20-fold jump in the signal is noticed from the unique working electrode configuration in contrast to the other electrode configurations. This demonstrates the potential of the sensor to have a significant increase in detection sensitivity for DNA and other biomolecules.

Advances in diagnostic microfluidics

Microfluidics is an emerging field in diagnostics that allows for extremely precise fluid control and manipulation, enabling rapid and high-throughput sample processing in integrated micro-scale medical systems. These platforms are well-suited for both standard clinical settings and point-of-care applications. The unique features of microfluidics-based platforms make them attractive for early disease diagnosis and real-time monitoring of the disease and therapeutic efficacy. In this chapter, we will first provide a background on microfluidic fundamentals, microfluidic fabrication technologies, microfluidic reactors, and microfluidic total-analysis-systems. Next, we will move into a discussion on the clinical applications of existing and emerging microfluidic platforms for blood analysis, and for diagnosis and monitoring of cancer and infectious disease. Together, this chapter should elucidate the potential that microfluidic systems have in the development of effective diagnostic technologies through a review of existing technologies and promising directions.

Microfluidics-enabled rapid manufacturing of hierarchical silica-magnetic microflower toward enhanced circulating tumor cell screening

The emergence of microfluidic techniques provides new opportunities for chemical synthesis and biomedical applications. Herein, we first develop a microfluidics-based flow and sustainable strategy to synthesize hierarchical silica-magnetic microflower with unique multilayered structure for the efficient capture of circulating tumor cells through our engineered microfluidic screening chip. The production of microflower materials can be realized within 94 milliseconds and a yield of nearly 5 grams per hour can be achieved. The enhanced bioaccessibility of such a multilayered microflower towards cancer cells (MCF-7 and MDA-MB-231) is demonstrated, and the cancer cell capture efficiency of this hierarchical immunomagnetic system in clinical blood samples is significantly increased compared with a standard CellSearch™ assay. These findings bring new insights for engineering functional micro-/nanomaterials in liquid biopsy.

Combined immunomagnetic capture coupled with ultrasensitive plasmonic detection of circulating tumor cells in blood

We demonstrate enhanced on-chip circulating tumor cell (CTC) detection through the incorporation of plasmonic-enhanced near-infrared (NIR) fluorescence screening. Specifically, the performance of plasmonic gold coated chips was evaluated on our previously reported immunomagnetic CTC capture system and compared to the performance of a regular chip. Three main performance metrics were evaluated: capture efficiency, capture reproducibility, and clinical efficacy. Use of the plasmonic chip to capture SK-BR-3 cells in PBS, resulted in a capture efficiency of 82%, compared to 76% with a regular chip. Both chips showed excellent capture reproducibility for all three cells lines evaluated (MCF-7, SK-BR-3, Colo 205) in both PBS and peripheral blood, with R2 values ranging from 0.983 to 0.996. Finally, performance of the plasmonic chip was evaluated on thirteen peripheral blood samples in patients with both breast and prostate cancer. The regular chip detected 2-8 cells per 5 mL of blood, while the plasmonic chip detected 8-85 cells per 5 mL of blood in parallel samples. In summary, we successfully demonstrate improved CTC capture and detection capabilities through use of plasmonic-enhanced near-infrared (NIR) fluorescence screening in both in vitro and ex vivo experiments. This work not only has the potential to improve clinical outcomes though improved CTC analysis, but also demonstrates successful interface design between plasmonic materials and cell capture for bioanalytical applications.

Blood-Based Cancer Biomarkers in Liquid Biopsy: A Promising Non-Invasive Alternative to Tissue Biopsy

Cancer is one of the greatest threats facing our society, being the second leading cause of death globally. Currents strategies for cancer diagnosis consist of the extraction of a solid tissue from the affected area. This sample enables the study of specific biomarkers and the genetic nature of the tumor. However, the tissue extraction is risky and painful for the patient and in some cases is unavailable in inaccessible tumors. Moreover, a solid biopsy is expensive and time consuming and cannot be applied repeatedly. New alternatives that overcome these drawbacks are rising up nowadays, such as liquid biopsy. A liquid biopsy is the analysis of biomarkers in a non-solid biological tissue, mainly blood, which has remarkable advantages over the traditional method; it has no risk, it is non-invasive and painless, it does not require surgery and reduces cost and diagnosis time. The most studied cancer non-invasive biomarkers are circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), and exosomes. These circulating biomarkers play a key role in the understanding of metastasis and tumorigenesis, which could provide a better insight into the evolution of the tumor dynamics during treatment and disease progression. Improvements in isolation technologies, based on a higher grade of purification of CTCs, exosomes, and ctDNA, will provide a better characterization of biomarkers and give rise to a wide range of clinical applications, such as early detection of diseases, and the prediction of treatment responses due to the discovery of personalized tumor-related biomarkers.

Liquid Biopsy in Colorectal Cancer-Current Status and Potential Clinical Applications

Colorectal cancer is one of the most frequent solid malignancies worldwide. The treatment is either surgical or multimodal and depends on the stage of the disease at diagnosis. Accurate disease assessment is thus of great importance for choosing the most optimal treatment strategy. However, the standard means of disease assessment by radiological imaging or histopathological analysis of the removed tumor tissue lack the sensitivity in detecting the early systemic spread of the disease. To overcome this deficiency, the concept of liquid biopsy from the peripheral blood of patients has emerged as a new, very promising diagnostic tool. In this article, we provide an overview of the current status of clinical research on liquid biopsy in colorectal cancer. We also highlight the clinical situations in which the concept might be of the greatest benefit for the management of colorectal cancer patients in the future.