Liquid biopsy: monitoring cancer-genetics in the blood

Isolation, Detection and Analysis of Circulating Tumour Cells: A Nanotechnological Bioscope

Cancer is one of the dreaded diseases to which a sizeable proportion of the population succumbs every year. Despite the tremendous growth of the health sector, spanning diagnostics to treatment, early diagnosis is still in its infancy. In this regard, circulating tumour cells (CTCs) have of late grabbed the attention of researchers in the detection of metastasis and there has been a huge surge in the surrounding research activities. Acting as a biomarker, CTCs prove beneficial in a variety of aspects. Nanomaterial-based strategies have been devised to have a tremendous impact on the early and rapid examination of tumor cells. This review provides a panoramic overview of the different nanotechnological methodologies employed along with the pharmaceutical purview of cancer. Initiating from fundamentals, the recent nanotechnological developments toward the detection, isolation, and analysis of CTCs are comprehensively delineated. The review also includes state-of-the-art implementations of nanotechnological advances in the enumeration of CTCs, along with future challenges and recommendations thereof.

Convenient exosome separation by phosphatidylserine targeting polymer brush materials

We report phosphatidylserine targeting polymer brush materials to selectively separate exosomes. This method provides an efficient separation strategy with ordinary centrifuge force, which improves the integrity and purity of the exosomes. Compared with the common methods, the content of contaminated lipoprotein in the resulting exosomes decreased obviously.

Identification of TP53 mutations in circulating tumour DNA in high grade serous ovarian carcinoma using next generation sequencing technologies

Plasma circulating tumour DNA (ctDNA) has been suggested to be a viable biomarker of response to treatment in patients with high grade serous ovarian carcinoma (HGSOC). TP53 mutations are present in more than 90% of HGSOCs but somatic variants are distributed across all exonic regions of the gene, requiring next generation sequencing (NGS) technologies for mutational analysis. In this study, we compared the suitability of the Accel (Swift) and Oncomine (ThermoFisher) panels for identification of TP53 mutations in ctDNA of HGSOC patients (N = 10). Only 6 patients (60%) were found to have TP53 mutations using the ACCEL panel but the addition of molecular tags in the Oncomine panel improved ctDNA detection with at least one mutation detected in all cases (100%). Orthogonal validation of the 14 somatic variants found by Oncomine, using droplet digital PCR, confirmed 79% (11/14) of the identified mutations. Overall, the Oncomine panel with unique molecular identifiers (UMI) appears more useful for ctDNA analysis in HGSOC.

Fabrication of Multilayer Microfluidic Arrays for Passive, Efficient DNA Trapping and Profiling

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.

A Microfluidic Approach for Enrichment and Single-Cell Characterization of Circulating Tumor Cells from Peripheral Blood

The emergence of enabling technologies for the analysis of circulating tumor cells has been shedding new lights into cancer management in the recent years. However, majority of the technologies developed suffer from excessive cost, time-consuming workflows, and reliance on specialized equipment and operators. Herein, we propose a simple workflow for the isolation and characterization of single circulating tumor cells using microfluidic devices. The entire process can be operated by a laboratory technician without relying on any microfluidic expertise and can be completed within few hours of sample collection.

A novel platform using homobifunctional hydrazide for enrichment and isolation of urinary circulating RNAs

Changes in specific circulating RNA (circRNA) expressions can serve as diagnostic noninvasive biomarkers for prostate cancer (PCa). However, there are still unmet needs, such as unclear types and roles of circRNAs, PCa detection in benign prostatic hyperplasia (BPH) by unstandardized methods, and limitations of sample volume capacity and low circRNA concentrations. This study reports a simple and rapid circRNA enrichment and isolation technique named "HAZIS-CirR" for the analysis of urinary circRNAs. The method utilizes homobifunctional hydrazides with amine-modified zeolite and polyvinylidene fluoride (PVDF) syringe filtration for combining electrostatic and covalent coupling and size-based filtration, and it offers instrument-free isolation of circRNAs in 20 min without volume limitation, thermoregulation, and lysis. HAZIS-CirR has high capture efficiency (82.03%-92.38%) and a 10-fold more sensitive detection limit (20 fM) than before enrichment (200 fM). The clinical utility of HAZIS-CirR is confirmed by analyzing circulating mRNAs and circulating miRNAs in 89 urine samples. Furthermore, three miRNA panels that differentiate PCa from BPH and control, PCa from control, and BPH from control, respectively, are established by comparing miRNA levels. HAZIS-CirR will be used as an optimal and established method for the enrichment and isolation of circRNAs as diagnostic, prognostic, and predictive biomarkers in human cancers.

Bronchoalveolar Lavage as Potential Diagnostic Specimens to Genetic Testing in Advanced Nonsmall Cell Lung Cancer

Background: There is limited knowledge on the yield of performing capture-based targeted ultradeep sequencing on bronchoalveolar lavage (BAL) specimens from advanced nonsmall cell lung cancer (NSCLC) patients. This study aimed to evaluate gene variations and performance characteristics in BAL and tissue specimens using targeted sequencing. Methods: This cohort study retrospectively enrolled 20 patients with advanced NSCLC. The variant detection percentage, correlation of tumor mutation burden (TMB), and allele frequency heterogeneity (AFH) were compared between paired BAL and tissue samples. A three-tiered system was also applied for the interpretation of gene variants according to the guidelines. Results: No statistical difference was observed in variant detection between BAL and tissue samples (P = .591 for variant tier and P = .409 for variant type). In general, BAL achieved higher detection rates in tier I variants (96.2% vs 84.6%) and gene fusions (75% vs 50%) compared with tissue samples; tissue samples had better variants detection rates for other variants, such as tier II (89.6% vs 76.0%), tier III (87.1% vs 72.6%), single nucleotide variant (SNV, 89.6% vs 76.5%), insertion/deletion/duplication (InDel, 74.6% vs 69.8%) and copy number variation (CNV, 93.8% vs 43.8%). Besides, there were significant correlations of TMB (R2 = 0.96, P < .001) and AFH (R2 = 0.87, P < .001) between BALs and paired tissues. Conclusions: The findings demonstrate that BAL may serve as a supplement in liquid biopsy for mutation detection and for routine utilization in clinical settings.

Kan Plazmasında Satellit-2 Tekrar Elementi DNA Dizilerinin Karakterizasyonu

Amaç: Son yıllarda tıp biliminin farklı disiplinlerinde sıkça karşılaşılan kavramlardan biri olan “sıvı biyopsi”, hastaların tanı, prognoz analizi ve tedaviye cevabını değerlendirme gibi konularda girişimsel doku biyopsisi yerine, kan ve çeşitli vücut sıvılarındaki moleküler ve epigenetik biyobelirteçlerin kullanılmasını içerir. Dolaşımda serbest halde dolaşan DNA’da (‘cell-free DNA’, cfDNA) kanser hücrelerine özgü gen mutasyonlarının saptanması, kanser hücrelerinin içeriğinin vücut sıvılarına geçtiğinin kesin kanıtı olarak kabul edilmektedir. cfDNA’nın bileşiminin belirlenmesine yönelik dizileme çalışmaları, perisentrik satellit DNA dizilerinin, cfDNA’da genom oranlarına kıyasla daha fazla oranda temsil edildiğini bildirmiştir. Bu çalışmada, kanser açısından spesifik dizilerin saptanması amacıyla, Sat-2 dizilerinin polimeraz zincir reaksiyonunda (PCR) çoğaltılmaları sonrasında daha detaylı karakterizasyonu amaçlanmıştır.Yöntem: Çalışmada, sağlıklı ve metastatik meme kanserli hastaların plazmalarından 1. ve 10. kromozoma spesifik Sat-2 dizileri PCR ile çoğaltıldıktan sonra, otomatik elektroforez sisteminde ayrıştırıldılar.Bulgular: Yapılan büyüklük analizinde, iki bölgeden çok sayıda amplikon oluştuğu, bunların yaklaşık %50’ni sırasıyla 143 ve 115 bç uzunluğunda ürünlerin oluşturduğu belirlenmiştir. Bu iki PCR amplikonunun miktarı meme kanserli hastalarda daha yüksek olarak hesaplandı. Onuncu kromozoma özgü 115 bç’lik fargman dışındaki Sat-2 dizileri açısından kontroller ile hastalar arasında önemli farklar olduğu belirlenmiştir.Sonuç: Çalışma kapsamında elde edilen bulgular, Sat-2 tekrar elementine ait DNA dizilerinin sekanslanması sonrası kansere spesifik hedef bölgelerin saptanabileceğini ortaya koymaktadır. 

Microfluidic Strategies for Extracellular Vesicle Isolation: Towards Clinical Applications

Extracellular vesicles (EVs) are double-layered lipid membrane vesicles released by cells. Currently, EVs are attracting a lot of attention in the biological and medical fields due to their role as natural carriers of proteins, lipids, and nucleic acids. Thus, they can transport useful genomic information from their parental cell through body fluids, promoting cell-to-cell communication even between different organs. Due to their functionality as cargo carriers and their protein expression, they can play an important role as possible diagnostic and prognostic biomarkers in various types of diseases, e.g., cancers, neurodegenerative, and autoimmune diseases. Today, given the invaluable importance of EVs, there are some pivotal challenges to overcome in terms of their isolation. Conventional methods have some limitations: they are influenced by the starting sample, might present low throughput and low purity, and sometimes a lack of reproducibility, being operator dependent. During the past few years, several microfluidic approaches have been proposed to address these issues. In this review, we summarize the most important microfluidic-based devices for EV isolation, highlighting their advantages and disadvantages compared to existing technology, as well as the current state of the art from the perspective of the use of these devices in clinical applications.

Serum-Exosome-Derived miRNAs Serve as Promising Biomarkers for HCC Diagnosis

BACKGROUND

Serum exosomes are emerging as key liquid biopsy biomarkers for the early diagnosis of cancer. However, the proportion and distribution of small RNA (sRNA) species from serum exosomes of hepatocellular carcinoma (HCC) patients remain unclear. Effective and reliable biomarkers for HCC diagnosis should be explored.

METHODS

In this study, we aimed to use sRNA sequencing to profile the sRNAs of serum exosomes in HCC and non-tumor donors. The serum exosomes of 124 HCC patients and 46 non-tumor donors were enrolled for detecting the values of the potential biomarkers for the diagnosis of HCC.

RESULTS

We found that miRNAs accounted for the maximal percentage of all types of sRNAs both in the serum exosomes of HCC patients and non-tumor donors. This indicated that the serum-exosome-derived microRNAs (miRNAs) were the most valuable as potential biomarkers in HCC diagnosis. Then, miRNAs were set as research candidates. In our Chinese cohorts, three serum-exosome-derived miRNAs (miR-122-5p, let-7d-5p, and miR-425-5p) could be promising biomarkers for distinguishing HCC patients from non-tumor donors. In addition, they were preferred for the early diagnosis of HCC. We also presented the base distribution of some novel serum-exosome-derived miRNAs and described the potential values as biomarkers.

CONCLUSIONS

The results suggested that the serum-exosome-derived miRNAs were the most crucial sRNA species and they highlighted the potential of serum-exosome-derived miRNAs as promising biomarkers for HCC diagnosis.

Tailored point-of-care biosensors for liquid biopsy in the field of oncology

In the field of cancer detection, technologies to analyze tumors using biomarkers circulating in fluids such as blood have developed rapidly based on liquid biopsy. A proactive approach to early cancer detection can lead to more effective treatments with minimal side effects and better long-term patient survival. However, early detection of cancer is hindered by the existing limitations of conventional cancer diagnostic methods. To enable early diagnosis and regular monitoring and improve automation, the development of integrated point-of-care (POC) and biosensors is needed. This is expected to fundamentally change the diagnosis, management, and monitoring of response to treatment of cancer. POC-based techniques will provide a way to avoid complications that occur after invasive tissue biopsy, such as bleeding, infection, and pain. The aim of this study is to provide a comprehensive view of biosensors and their clinical relevance in oncology for the detection of biomarkers with liquid biopsies of proteins, miRNA, ctDNA, exosomes, and cancer cells. The preceding discussion also illustrates the changing landscape of liquid biopsy-based cancer diagnosis through nanomaterials, machine learning, artificial intelligence, wearable devices, and sensors, many of which apply POC design principles. With the advent of sensitive, selective, and timely detection of cancer, we see the field of POC technology for cancer detection and treatment undergoing a positive paradigm shift in the foreseeable future.

Detection of circulating KRAS mutant DNA in extracellular vesicles using droplet digital PCR in patients with colon cancer

Background

Extracellular vesicles secreted by tumor cells contain double-stranded DNA called extracellular vesicle DNA (evDNA). EvDNA is genomic DNA that reflects cancer driver mutations. However, the significance of evDNA analysis in the diagnosis and surveillance of colon cancer remains unclear. This study aimed to investigate the clinical utility of extracellular vesicles and evDNA isolated from the plasma of colon cancer patients harboring KRAS G12D and G13D mutations.

Methods

Cell-free DNA (cfDNA) and evDNA were collected from the plasma of 30 patients with colon cancer. KRAS mutation status (G12D and G13D) was detected using a droplet digital polymerase chain reaction assay (ddPCR). Sensitivity and specificity were evaluated in patients with wild-type KRAS tumors. Mutation status was correlated with carcinoembryonic antigen (CEA) levels and overall survival (OS).

Results

Thirty cfDNA and evDNA pairs showed a KRAS fractional abundance (FA) ranging from 0 to 45.26% and 0 to 83.81%, respectively. When compared with eight wild-type KRAS samples, cfDNA exhibited 70% sensitivity and 100% specificity, whereas evDNA achieved 76.67% sensitivity and 100% specificity. The concentration of evDNA was significantly lower than that of cfDNA, but it obtained a higher FA than cfDNA, while showing a positive correlation with CEA.

Conclusions

Our findings demonstrate the feasibility of evDNA as a complementary tool to aid current methods of patient evaluation in the diagnosis and surveillance of colon cancer.

Antenna-enhanced mid-infrared detection of extracellular vesicles derived from human cancer cell cultures

BACKGROUND

Extracellular Vesicles (EVs) are sub-micrometer lipid-bound particles released by most cell types. They are considered a promising source of cancer biomarkers for liquid biopsy and personalized medicine due to their specific molecular cargo, which provides biochemical information on the state of parent cells. Despite this potential, EVs translation process in the diagnostic practice is still at its birth, and the development of novel medical devices for their detection and characterization is highly required.

RESULTS

In this study, we demonstrate mid-infrared plasmonic nanoantenna arrays designed to detect, in the liquid and dry phase, the specific vibrational absorption signal of EVs simultaneously with the unspecific refractive index sensing signal. For this purpose, EVs are immobilized on the gold nanoantenna surface by immunocapture, allowing us to select specific EV sub-populations and get rid of contaminants. A wet sample-handling technique relying on hydrophobicity contrast enables effortless reflectance measurements with a Fourier-transform infrared (FTIR) spectro-microscope in the wavelength range between 10 and 3 µm. In a proof-of-principle experiment carried out on EVs released from human colorectal adenocarcinoma (CRC) cells, the protein absorption bands (amide-I and amide-II between 5.9 and 6.4 µm) increase sharply within minutes when the EV solution is introduced in the fluidic chamber, indicating sensitivity to the EV proteins. A refractive index sensing curve is simultaneously provided by our sensor in the form of the redshift of a sharp spectral edge at wavelengths around 5 µm, where no vibrational absorption of organic molecules takes place: this permits to extract of the dynamics of EV capture by antibodies from the overall molecular layer deposition dynamics, which is typically measured by commercial surface plasmon resonance sensors. Additionally, the described metasurface is exploited to compare the spectral response of EVs derived from cancer cells with increasing invasiveness and metastatic potential, suggesting that the average secondary structure content in EVs can be correlated with cell malignancy.

CONCLUSIONS

Thanks to the high protein sensitivity and the possibility to work with small sample volumes-two key features for ultrasensitive detection of extracellular vesicles- our lab-on-chip can positively impact the development of novel laboratory medicine methods for the molecular characterization of EVs.

The Role of Cell-Free DNA in Cancer Treatment Decision Making

The aim of this review is to evaluate the present status of the use of cell-free DNA and its fraction of circulating tumor DNA (ctDNA) because this year July 2022, an ESMO guideline was published regarding the application of ctDNA in patient care. This review is for clinical oncologists to explain the concept, the terms used, the pros and cons of ctDNA; thus, the technical aspects of the different platforms are not reviewed in detail, but we try to help in navigating the current knowledge in liquid biopsy. Since the validated and adequately sensitive ctDNA assays have utility in identifying actionable mutations to direct targeted therapy, ctDNA may be used for this soon in routine clinical practice and in other different areas as well. The cfDNA fragments can be obtained by liquid biopsy and can be used for diagnosis, prognosis, and selecting among treatment options in cancer patients. A great proportion of cfDNA comes from normal cells of the body or from food uptake. Only a small part (<1%) of it is related to tumors, originating from primary tumors, metastatic sites, or circulating tumor cells (CTCs). Soon the data obtained from ctDNA may routinely be used for finding minimal residual disease, detecting relapse, and determining the sites of metastases. It might also be used for deciding appropriate therapy, and/or emerging resistance to the therapy and the data analysis of ctDNA may be combined with imaging or other markers. However, to achieve this goal, further clinical validations are inevitable. As a result, clinicians should be aware of the limitations of the assays. Of course, several open questions are still under research and because of it cfDNA and ctDNA testing are not part of routine care yet.

Evolution of RAS Mutations in Cell-Free DNA of Patients with Tissue RAS Wild-Type Metastatic Colorectal Cancer Receiving First-Line Treatment: The PERSEIDA Study

The serial analysis of cell-free DNA (cfDNA) enables minimally invasive monitoring of tumor evolution, providing continuous genetic information. PERSEIDA was an observational, prospective study assessing the cfDNA RAS (KRAS/NRAS) mutational status evolution in first-line, metastatic CRC, RAS wild-type (according to baseline tumor tissue biopsy) patients. Plasma samples were collected before first-line treatment, after 20 ± 2 weeks, and at disease progression. One hundred and nineteen patients were included (102 received panitumumab and chemotherapy as first-line treatment-panitumumab subpopulation). Fifteen (12.6%) patients presented baseline cfDNA RAS mutations (n = 14 [13.7%], panitumumab subpopulation) (mutant allele fraction ≥0.02 for all results). No patients presented emergent mutations (cfDNA RAS mutations not present at baseline) at 20 weeks. At disease progression, 11 patients (n = 9; panitumumab subpopulation) presented emergent mutations (RAS conversion rate: 19.0% [11/58]; 17.7% [9/51], panitumumab subpopulation). In contrast, three (5.2%) patients presenting baseline cfDNA RAS mutations were RAS wild-type at disease progression. No significant associations were observed between overall response rate or progression-free survival and cfDNA RAS mutational status in the total panitumumab subpopulation. Although, in patients with left-sided tumors, a significantly longer progression-free survival was observed in cfDNA RAS wild-type patients compared to those presenting cfDNA RAS mutations at any time. Continuous evaluation of RAS mutations may provide valuable insights on tumor molecular dynamics that can help clinical practice.

Cutting-Edge Developments in Oncology Research

The field of oncology research has made many successful advances, and new discoveries have started making headlines. As an example, the identification of immune checkpoint inhibition mechanisms in carcinogenic cells led to the development of immunoassays, which have helped many cancer convalescents recover. This article covers the most advanced cutting-edge areas of cancer research: exosomes, microbiomes, immunotherapy, nanocarriers, and organoids. Research on exosomes advances cancer detection and treatment modalities, as well as further understanding of mechanisms that regulate carcinogen cell division, proliferation, invasion, and metastasis. Microbiome consents the researchers to understand the disease cancer. Immunotherapy is the third method in the treatment of cancer. Organoid biology will be further expanded with the aim of translating research into customized therapeutic therapies. Nanocarriers enable cancer specific drug delivery by inherent unreceptive targeting phenomena and implemented active targeting strategies. These areas of research may also bring about the advent of the latest cancer treatments in the future. Malignant infections are one of the leading grounds for demise in the society. Patients are treated with surgery, radiation, and chemotherapy. In chemotherapy, the malignant cells are destroyed and the tumor burden is reduced. However, in most cases, resistance to chemotherapy develops. Therefore, there is a constant need for new additional treatment modalities and chemotherapeutic complex rules. Due to the rapid development in cancer research, I can only mention a few goals and treatment options that I have chosen; However, this review specializes in new and admirable significant strategies and compounds.

Digital Decoding of Single Extracellular Vesicle Phenotype Differentiates Early Malignant and Benign Lung Lesions

Accurate identification of malignant lung lesions is a prerequisite for rational clinical management to reduce morbidity and mortality of lung cancer. However, classification of lung nodules into malignant and benign cases is difficult as they show similar features in computer tomography and sometimes positron emission tomography imaging, making invasive tissue biopsies necessary. To address the challenges in evaluating indeterminate nodules, the authors investigate the molecular profiles of small extracellular vesicles (sEVs) in differentiating malignant and benign lung nodules via a liquid biopsy-based approach. Aiming to characterize phenotypes between malignant and benign groups, they develop a single-molecule-resolution-digital-sEV-counting-detection (DECODE) chip that interrogates three lung-cancer-associated sEV biomarkers and a generic sEV biomarker to create sEV molecular profiles. DECODE capturessEVs on a nanostructured pillar chip, confines individual sEVs, and profiles sEV biomarker expression through surface-enhanced Raman scattering barcodes. The author utilize DECODE to generate a digitally acquired sEV molecular profiles in a cohort of 33 people, including patients with malignant and benign lung nodules, and healthy individuals. Significantly, DECODE reveals sEV-specific molecular profiles that allow the separation of malignant from benign (area under the curve, AUC = 0.85), which is promising for non-invasive characterisation of lung nodules found in lung cancer screening and warrants further clinincal validaiton with larger cohorts.

Pancreatic Tumorigenesis: Precursors, Genetic Risk Factors and Screening

Pancreatic cancer (PC) is a highly malignant and aggressive tumor. Despite medical advancement, the silent nature of PC results in only 20% of all cases considered resectable at the time of diagnosis. It is projected to become the second leading cause in 2030. Most pancreatic cancer cases are diagnosed in the advanced stages. Such cases are typically unresectable and are associated with a 5-year survival of less than 10%. Although there is no guideline consensus regarding recommendations for screening for pancreatic cancer, early detection has been associated with better outcomes. In addition to continued utilization of imaging and conventional tumor markers, clinicians should be aware of novel testing modalities that may be effective for early detection of pancreatic cancer in individuals with high-risk factors. The pathogenesis of PC is not well understood; however, various modifiable and non-modifiable factors have been implicated in pancreatic oncogenesis. PC detection in the earlier stages is associated with better outcomes; nevertheless, most oncological societies do not recommend universal screening as it may result in a high false-positive rate. Therefore, targeted screening for high-risk individuals represents a reasonable option. In this review, we aimed to summarize the pathogenesis, genetic risk factors, high-risk population, and screening modalities for PC.

Lung cancer subtype diagnosis using weakly-paired multi-omics data

MOTIVATION

Cancer subtype diagnosis is crucial for its precise treatment and different subtypes need different therapies. Although the diagnosis can be greatly improved by fusing multiomics data, most fusion solutions depend on paired omics data, which are actually weakly paired, with different omics views missing for different samples. Incomplete multiview learning-based solutions can alleviate this issue but are still far from satisfactory because they: (i) mainly focus on shared information while ignore the important individuality of multiomics data and (ii) cannot pick out interpretable features for precise diagnosis.

RESULTS

We introduce an interpretable and flexible solution (LungDWM) for Lung cancer subtype Diagnosis using Weakly paired Multiomics data. LungDWM first builds an attention-based encoder for each omics to pick out important diagnostic features and extract shared and complementary information across omics. Next, it proposes an individual loss to jointly extract the specific information of each omics and performs generative adversarial learning to impute missing omics of samples using extracted features. After that, it fuses the extracted and imputed features to diagnose cancer subtypes. Experiments on benchmark datasets show that LungDWM achieves a better performance than recent competitive methods, and has a high authenticity and good interpretability.

AVAILABILITY AND IMPLEMENTATION

The code is available at http://www.sdu-idea.cn/codes.php?name=LungDWM.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Preliminary Experience of Liquid Biopsy in Lung Cancer Compared to Conventional Assessment: Light and Shadows

Purpose: To assess the qualitative relationship between liquid biopsy and conventional tissue biopsy. As a secondary target, we evaluated the relationship between the liquid biopsy results and the T stage, N stage, M stage, and compared to grading. Methods: The Local Ethics Committee of the “Università degli Studi della Campania Luigi Vanvitelli”, with the internal resolution number 24997/2020 of 12.11.2020, approved this spontaneous prospective study. According to the approved protocol, patients with lung cancer who underwent Fine-Needle Aspiration Cytology (FNAC), CT-guided biopsy, and liquid biopsy were enrolled. A Yates chi-square test was employed to analyze differences in percentage values of categorical variables. A p-value < 0.05 was considered statistically significant. Data analysis was performed using the Matlab Statistic Toolbox (The MathWorks, Inc., Natick, MA, USA). Results: When a genetic mutation is present on the pathological examination, this was also detected on the liquid biopsy. ROS1 and PDL1 mutations were found in 2/29 patients, while EGFR Exon 21 was identified in a single patient. At liquid biopsy, 26 mutations were identified in the analyzed samples. The mutations with the highest prevalence rate in the study populations were: ALK (Ile1461Val), found in 28/29 patients (96.6%), EML4 (Lys398Arg), identified in 16/29 (55.2%) patients, ALK (Asp1529Glu), found in 14/29 (48.3%) patients, EGFR (Arg521Lys), found in 12/29 (41.4%) patients, ROS (Lys2228Gln), identified in 11/29 (37.9%) patients, ROS (Arg167Gln) and ROS (Ser2229Cys), identified in 10/29 (34.5%) patients, ALK (Lys1491Arg) and PIK3CA (Ile391Met), identified in 8/29 (27.6%) patients, ROS (Thr145Pro), identified in 6/29 (20.7%) patients, and ROS (Ser1109Leu), identified in 4/29 (13.8%) patients. No statistically significant differences can be observed in the mutation rate between the adenocarcinoma population and the squamous carcinoma population (p > 0.05, Yates chi-square test). Conclusions: We showed that, when a genetic mutation was detected in pathological examination, this was always detected by liquid biopsy, demonstrating a very high concordance rate of genomic testing between tissues and their corresponding mutations obtained by liquid biopsy, without cases of false-negative results. In addition, in our study, liquid biopsy highlighted 26 mutations, with the prevalence of ALK mutation in 96.6% of patients, supporting the idea that this approach could be an effective tool in cases with insufficient tumor tissue specimens or in cases where tissue specimens are not obtainable.

Blood platelets as an RNA biomarker platform for neuro-oncological diseases

Blood-based liquid biopsies are an upcoming approach for earlier cancer detection, diagnostics, prognostics, therapy-response prediction, and therapy monitoring, including in patients with tumors of the central nervous system. Among these, liquid biopsies are plasma-derived markers such as cell-free DNA, RNA and proteins, extracellular vesicles, circulating glioma cells, immune cells, and blood platelets. Blood platelets are involved in the local and systemic response to the presence of cancer, thereby sequestering and splicing RNAs, which may be clinically useful as blood-based biomarkers. In this review, we discuss the available literature regarding the role of blood platelets in gliomas and provide suggestions for future research efforts.

Diagnostic performance of circulating tumor DNA as a minimally invasive biomarker for hepatocellular carcinoma: a systematic review and meta-analysis

Purpose

This study aimed to assess the diagnostic performance of circulating tumor DNA (ctDNA) in hepatocellular carcinoma (HCC).

Materials and Methods

We enrolled all relevant studies published up to 5 January 2022. Three primary subgroups were investigated: qualitative or quantitative ctDNA analyses, combined alpha-fetoprotein (AFP), and ctDNA assay. In addition to the three primary subgroups, we also evaluated the diagnostic value of methylated SEPTIN9 (mSEPT9), which has been studied extensively in the diagnosis of hepatocellular carcinoma. After a search based on four primary databases, we used a bivariate linear mixed model to analyze the pooled sensitivity (SEN), specificity (SPE), positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR). We also plotted hierarchical summary receiver operating characteristics (HSROC) and utilized lambda as well as the area under the curve (AUC) to create summary receiver operating characteristic (SROC) curves to estimate the diagnostic value of ctDNA.

Results

A total of 59 qualified articles with 9,766 subjects were incorporated into our meta-analysis. The integrated SEN, SPE, and DOR in the qualitative studies were 0.50 (95% CI [0.43-0.56]), 0.90 (95% CI [0.86-0.93]), and 8.72 (95% CI [6.18-12.32]), respectively, yielding an AUC of 0.78 and lambda of 1.93 (95% CI [1.56-2.33]). For quantitative studies, the corresponding values were 0.69 (95% CI [0.63-0.74]), 0.84 (95% CI [0.77-0.89]), 11.88 (95% CI [7.78-18.12]), 0.81, and 2.32 (95% CI [1.96-2.69]), respectively. Six studies were included to evaluate the SETP9 methylation, which yielded an AUC of 0.86, a SEN of 0.80 (95% CI [0.71-0.87]), and a SPE of 0.77 (95% CI [0.68-0.85]). Likewise, ctDNA concentration yielded an AUC of 0.73, with a SEN of 0.63 (95% CI [0.56-0.70]) and a SPE of 0.86 (95% CI [0.74-0.93]). AFP combined with ctDNA assay resulted in an AUC of 0.89, with a SEN of 0.82 (95% CI [0.77-0.86]) and a SPE of 0.84 (95% CI [0.76-0.90]).

Conclusion

This study shows that circulating tumor DNA, particularly mSEPT9, shows promising diagnostic potential in HCC; however, it is not enough to diagnose HCC independently, and ctDNA combined with conventional assays such as AFP can effectively improve diagnostic performance.

Comparative analysis of capture methods for genomic profiling of circulating tumor cells in colorectal cancer

The genomic profiling of circulating tumor cells (CTCs) in the bloodstream should provide clinically relevant information on therapeutic efficacy and help predict cancer survival. Here, we contrasted the genomic profiles of CTC pools recovered from metastatic colorectal cancer (mCRC) patients using different enrichment strategies (CellSearch, Parsortix, and FACS). Mutations inferred in the CTC pools differed depending on the enrichment strategy and, in all cases, represented a subset of the mutations detected in the matched primary tumor samples. However, the CTC pools from Parsortix, and in part, CellSearch, showed diversity estimates, mutational signatures, and drug-suitability scores remarkably close to those found in matching primary tumor samples. In addition, FACS CTC pools were enriched in apparent sequencing artifacts, leading to much higher genomic diversity estimates. Our results highlight the utility of CTCs to assess the genomic heterogeneity of individual tumors and help clinicians prioritize drugs in mCRC.

An Exosome-based Transcriptomic Signature for Noninvasive, Early Detection of Patients With Pancreatic Ductal Adenocarcinoma: A Multicenter Cohort Study

BACKGROUND & AIMS

Pancreatic ductal adenocarcinoma (PDAC) incidence is rising worldwide, and most patients present with an unresectable disease at initial diagnosis. Measurement of carbohydrate antigen 19-9 (CA19-9) levels lacks adequate sensitivity and specificity for early detection; hence, there is an unmet need to develop alternate molecular diagnostic biomarkers for PDAC. Emerging evidence suggests that tumor-derived exosomal cargo, particularly micro RNAs (miRNAs), offer an attractive platform for the development of cancer-specific biomarkers. Herein, genomewide profiling in blood specimens was performed to develop an exosome-based transcriptomic signature for noninvasive and early detection of PDAC.

METHODS

Small RNA sequencing was undertaken in a cohort of 44 patients with an early-stage PDAC and 57 nondisease controls. Using machine-learning algorithms, a panel of cell-free (cf) and exosomal (exo) miRNAs were prioritized that discriminated patients with PDAC from control subjects. Subsequently, the performance of the biomarkers was trained and validated in independent cohorts (n = 191) using quantitative reverse transcription polymerase chain reaction (qRT-PCR) assays.

RESULTS

The sequencing analysis initially identified a panel of 30 overexpressed miRNAs in PDAC. Subsequently using qRT-PCR assays, the panel was reduced to 13 markers (5 cf- and 8 exo-miRNAs), which successfully identified patients with all stages of PDAC (area under the curve [AUC] = 0.98 training cohort; AUC = 0.93 validation cohort); but more importantly, was equally robust for the identification of early-stage PDAC (stages I and II; AUC = 0.93). Furthermore, this transcriptomic signature successfully identified CA19-9 negative cases (<37 U/mL; AUC = 0.96), when analyzed in combination with CA19-9 levels, significantly improved the overall diagnostic accuracy (AUC = 0.99 vs AUC = 0.86 for CA19-9 alone).

CONCLUSIONS

In this study, an exosome-based liquid biopsy signature for the noninvasive and robust detection of patients with PDAC was developed.

Recent Advances in Exosomal miRNA Biosensing for Liquid Biopsy

As a noninvasive detection technique, liquid biopsy plays a valuable role in cancer diagnosis, disease monitoring, and prognostic assessment. In liquid biopsies, exosomes are considered among the potential biomarkers because they are important bioinformation carriers for intercellular communication. Exosomes transport miRNAs and, thus, play an important role in the regulation of cell growth and function; therefore, detection of cancer cell-derived exosomal miRNAs (exo-miRNAs) gives effective information in liquid biopsy. The development of sensitive, convenient, and reliable exo-miRNA assays will provide new perspectives for medical diagnosis. This review presents different designs and detection strategies of recent exo-miRNA assays in terms of signal transduction and amplification, as well as signal detection. In addition, this review outlines the current attempts at bioassay methods in liquid biopsies. Lastly, the challenges and prospects of exosome bioassays are also considered.

Direct capture and sequencing reveal ultra-short single-stranded DNA in biofluids

Cell-free DNA (cfDNA) has become the predominant analyte of liquid biopsy; however, recent studies suggest the presence of subnucleosomal-sized DNA fragments in circulation that are likely single-stranded. Here, we report a method called direct capture and sequencing (DCS) tailored to recover such fragments from biofluids by directly capturing them using short degenerate probes followed by single strand-based library preparation and next-generation sequencing. DCS revealed a new DNA population in biofluids, named ultrashort single-stranded DNA (ussDNA). Evaluation of the size distribution and abundance of ussDNA manifested generality of its presence in humans, animal species, and plants. In humans, red blood cells were found to contain abundant ussDNA; plasma-derived ussDNA exhibited modal size at 50 nt. This work reports the presence of an understudied DNA population in circulation, and yet more work is awaiting to study its generation mechanism, tissue of origin, disease implications, etc.

Genomic Instability in Cerebrospinal Fluid Cell-Free DNA Predicts Poor Prognosis in Solid Tumor Patients with Meningeal Metastasis

Simple Summary

We established a genomic instability score using unfiltered sequencing data from meningeal metastasis (MM) cell-free circulating tumor DNA (ctDNA) samples and found that substantial genomic instability (GI) was present in cerebrospinal fluid ctDNA rather than plasma ctDNA, implying that MM lesions have a significantly increased GI status compared to primary tumors or extracranial metastatic lesions, which may suggest tumor clonal evolution. We also found that high GI status was an independent poor prognostic factor in lung adenocarcinoma MM patients, including meningeal metastasis-free survival (MFS) and overall survival (OS). Considering that genomically unstable tumors are more sensitive to PARP inhibitors, targeting GI alone or in combination with conventional therapy may be a promising treatment strategy for solid tumor patients with MM.

Abstract

Genomic instability (GI), which leads to the accumulation of DNA loss, gain, and rearrangement, is a hallmark of many cancers such as lung cancer, breast cancer, and colon cancer. However, the clinical significance of GI has not been systematically studied in the meningeal metastasis (MM) of solid tumors. Here, we collected both cerebrospinal fluid (CSF) and plasma samples from 56 solid tumor MM patients and isolated cell-free ctDNA to investigate the GI status using a next-generation sequencing-based comprehensive genomic profiling of 543 cancer-related genes. According to the unfiltered heterozygous mutation data-derived GI score, we found that 37 (66.1%) cases of CSF and 3 cases (6%) of plasma had a high GI status, which was further validated by low-depth whole-genome sequencing analysis. It is demonstrated that a high GI status in CSF was associated with poor prognosis, high intracranial pressure, and low Karnofsky performance status scores. More notably, a high GI status was an independent poor prognostic factor of poor MM-free survival and overall survival in lung adenocarcinoma MM patients. Furthermore, high occurrences of the co-mutation of TP53/EGFR, TP53/RB1, TP53/ERBB2, and TP53/KMT2C were found in MM patients with a high GI status. In summary, the GI status in CSF ctDNA might be a valuable prognostic indicator in solid tumor patients with MM.

Attogram-level light-induced antigen-antibody binding confined in microflow

The analysis of trace amounts of proteins based on immunoassays and other methods is essential for the early diagnosis of various diseases such as cancer, dementia, and microbial infections. Here, we propose a light-induced acceleration of antigen-antibody reaction of attogram-level proteins at the solid-liquid interface by tuning the laser irradiation area comparable to the microscale confinement geometry for enhancing the collisional probability of target molecules and probe particles with optical force and fluidic pressure. This principle was applied to achieve a 102-fold higher sensitivity and ultrafast specific detection in comparison with conventional protein detection methods (a few hours) by omitting any pretreatment procedures; 47-750 ag of target proteins were detected in 300 nL of sample after 3 minutes of laser irradiation. Our findings can promote the development of proteomics and innovative platforms for high-throughput bio-analyses under the control of a variety of biochemical reactions.

The evolving role of liquid biopsy in lung cancer

Liquid biopsy has revolutionized the management of cancer patients. In particular, liquid biopsy-based testing has proven to be highly beneficial for identifying actionable cancer markers, especially when solid tissue biopsies are insufficient or unattainable. Beyond the predictive role, liquid biopsy may be a useful tool for comprehensive tumor genotyping, identification of emergent resistance mechanisms, monitoring of minimal residual disease, early detection, and cancer interception. The application of next generation sequencing to liquid biopsy has led to the "quantum leap" of predictive molecular pathology. Here, we review the evolving role of liquid biopsy in lung cancer.

Bioplatforms in liquid biopsy: advances in the techniques for isolation, characterization and clinical applications

Tissue biopsy analysis has conventionally been the gold standard for cancer prognosis, diagnosis and prediction of responses/resistances to treatments. The existing biopsy procedures used in clinical practice are, however, invasive, painful and often associated with pitfalls like poor recovery of tumor cells and infeasibility for repetition in single patients. To circumvent these limitations, alternative non-invasive, rapid and economical, yet sturdy, consistent and dependable, biopsy techniques are required. Liquid biopsy is an emerging technology that fulfills these criteria and potentially much more in terms of subject-specific real-time monitoring of cancer progression, determination of tumor heterogeneity and treatment responses, and specific identification of the type and stages of cancers. The present review first briefly revisits the state-of-the-art technique of liquid biopsy and then proceeds to address in detail, the advances in the potential clinical applications of four major biological agencies present in liquid biopsy samples (circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), exosomes and tumor-educated platelets (TEPs)). Finally, the authors conclude with the limitations that need to be addressed in order for liquid biopsy to effectively replace the conventional invasive biopsy methods in the clinical settings.

Liquid biopsy using ascitic fluid and pleural effusion supernatants for genomic profiling in gastrointestinal and lung cancers

Background

Precision medicine highlights the importance of incorporating molecular genetic testing into standard clinical care. Next-generation sequencing can detect cancer-specific gene mutations, and molecular-targeted drugs can be designed to be effective for one or more specific gene mutations. For patients with special site metastases, it is particularly important to use appropriate samples for genetic profiling. This study aimed to determine whether genomic profiling using ASC and PE is effective in detecting genetic mutations.

Methods

Tissues, plasma, ascites (ASC) supernatants, and pleural effusion (PE) samples from gastrointestinal cancer patients with peritoneal metastasis and lung cancer patients with pleural metastasis were collected for comprehensive genomic profiling. The samples were subjected to next-generation sequencing using a panel of 59 or 1021 cancer-relevant genes panel.

Results

A total of 156 tissues, 188 plasma samples, 45 ASC supernatants, and 1 PE samples from 304 gastrointestinal cancer patients and 446 PE supernatants, 122 tissues, 389 plasma samples, and 45 PE sediments from 407 lung cancer patients were analyzed. The MSAF was significantly higher in ASC and PE supernatant than that in plasma ctDNA (50.00% vs. 3.00%, p < 0.0001 and 28.5% vs. 1.30%, p < 0.0001, respectively). The ASC supernatant had a higher actionable mutation rate and more actionable alterations than the plasma ctDNA in 26 paired samples. The PE supernatant had a higher total actionable mutation rate than plasma (80.3% vs. 48.4%, p < 0.05). The PE supernatant had a higher frequency of uncommon variations than the plasma regardless of distant organ metastasis.

Conclusion

ASC and PE supernatants could be better alternative samples when tumor tissues are not available, especially in patients with only peritoneal or pleural metastases.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-022-09922-5.

Enrichment of Cancer Cells Based on Antibody-Free Selective Cell Adhesion

Blood-compatible and cell-adhering polymer materials are extremely useful for regenerative medicine and disease diagnosis. (Meth)acryl polymers with high hydrophilicity have been widely used in industries, and attempts to apply these polymers in the medical field are frequently reported. We focused on crosslinked polymer films prepared using bifunctional monomers, which are widely used as coating materials, and attempted to alter the cell adhesion behavior while maintaining blood compatibility by changing the chemical structure of the crosslinker. Four bifunctional monomers were studied, three of which were found to be blood-compatible polymers and to suppress platelet adhesion. The adhesion behavior of cancer cells to polymer films varied; moreover, the cancer model cells MCF-7 [EpCAM(+)] and MDA-MB-231 [EpCAM (-)], with different expression levels of epithelial cell adhesion molecule (EpCAM), showed distinct adhesion behavior for each material. We suggest that a combination of these materials has the potential to selectively capture and enrich highly metastatic cancer cells.

Biomarker potential of the GRP78 cell-free RNA in endometrial cancer

Background

Circulating tumor cells represent an opportunity for the assessment of early recurrent disease or for real-time tracing of cancer. Glucose Regulated Protein 78 (GRP78) is known in the literature as a stress factor in endometrial cancer. We aimed to investigate the importance of the gene by targeting tumor traces circulating in the cell fluids of patients with Type 1 endometrial cancer, examining cell-free RNAs in patients’ samples and performing ROC analysis.

Methodology

In this study, 32 endometrial cancer patients and 20 controls were included. This in vitro study evaluated, the GRP78 cell-free mRNA expression levels in endometrial cancer patients, by quantitative real-time polymerase chain reaction qRT–PCR Light Cycler. Receiver operating characteristic (ROC) analysis is a tool used to identify the precision of a diagnostic test or prediction model. In our study, we investigated whether the expression levels of cell-free GRP78 mRNA could be used as a diagnostic criterion.

Results

The ROC curve results for endometrial cancer diagnostic criterion of cfRNA GRP78 mRNA indicated quite a significant value (p < 0.001).

Conclusion

Current findings show that cell-free mRNA GRP78 is now a criterion that can be used together with smear mRNA GRP78 without the need for invasive methods in endometrial cancer studies.

Label-Free Sensing with Metal Nanostructure-Based Surface-Enhanced Raman Spectroscopy for Cancer Diagnosis

Surface-Enhanced Raman Spectroscopy (SERS) is a powerful analytical technique for the detection of small analytes with great potential for medical diagnostic applications. Its high sensitivity and excellent molecular specificity, which stems from the unique fingerprint of molecular species, have been applied toward the detection of different types of cancer. The noninvasive and rapid detection offered by SERS highlights its applicability for point-of-care (PoC) deployment for cancer diagnosis, screening, and staging, as well as for predicting tumor recurrence and treatment monitoring. This review provides an overview of the progress in label-free (direct) SERS-based chemical detection for cancer diagnosis with the main focus on the advances in the design and preparation of SERS substrates on the basis of metal nanoparticle structures formed via bottom-up strategies. It begins by introducing a synopsis of the working principles of SERS, including key chemometric approaches for spectroscopic data analysis. Then it introduces the advances of label-free sensing with SERS in cancer diagnosis using biofluids (blood, urine, saliva, sweat) and breath as the detection media. In the end, an outlook of the advances and challenges in cancer diagnosis via SERS is provided.

Bimetallic Metal-Organic Framework Fe/Co-MIL-88(NH2) Exhibiting High Peroxidase-like Activity and Its Application in Detection of Extracellular Vesicles

Metal-organic frameworks (MOFs) have many attractive features, including tunable composition, rigid structure, controllable pore size, and large specific surface area, and thus are highly applicable in molecular analysis. Depending on the MOF structure, a high number of unsaturated metal sites can be exposed to catalyze chemical reactions. In the present work, we report that using both Co(II) and Fe(III) to prepare the MIL-88(NH₂) MOF, we can produce the bimetallic MOF that can catalyze the conversion of 3,3',5,5″-tetramethylbenzidine (TMB) to a color product through a reaction with H₂O₂ at a higher reaction rate than the monometallic Fe-MIL-88(NH₂). The Michaelis constants (K_m) of the catalytic reaction for TMB and H₂O₂ are 3-5 times smaller, and the catalytic constants (k_cat) are 5-10 times higher than those of the horseradish peroxidase (HRP), supporting ultrahigh peroxidase-like activity. These values are also much more superior to those of the HRP-mimicking MOFs reported previously. Interestingly, the bimetallic MOF can be coupled with glucose oxidase (GOx) to trigger the cascade enzymatic reaction for highly sensitive detection of extracellular vesicles (EVs), a family of important biomarkers. Through conjugation to the aptamer that recognizes the marker protein on EV surface, the MOF can help isolate the EVs from biological matrices, which are subsequently labeled by GOx via antibody recognition. The cascade enzymatic reaction between MOF and GOx enables the detection of EVs at a concentration as low as 7.8 × 10⁴ particles/mL. The assay can be applied to monitor EV secretion by cultured cells and also can successfully detect the different EV quantities in the sera samples collected from cancer patients and healthy controls. Overall, we prove that the bimetallic Fe/Co-MIL-88(NH₂) MOF, with its high peroxidase activity and high biocompatibility, is a valuable tool deployable in clinical assays to facilitate disease diagnosis and prognosis.

Detection of clinically-relevant <em>EGFR</em> variations in <em>de novo</em> small cell lung carcinoma by droplet digital PCR

Targeted therapy that utilizes tyrosine kinase inhibitors (TKIs), specific to epidermal growth factor receptors (EGFR) has changed the landscape of treatment of non-small cell lung cancer (NSCLC). The success or failure of this approach depends on presence of certain variations in the tyrosine kinase domain of EGFR gene. Generally, patients diagnosed with Small cell lung cancer (SCLC) are considered ineligible for TKI therapy owing to the absence of EGFR variations. . However, there is evidence of these variations being detected in SCLCs, both in de-novo and in transformed SCLCs (TKI-treated adenocarcinomas). Despite the presence of clinically-relevant EGFR variations in SCLCs, the response to TKIs has been inconsistent.  Liquid biopsy is a well-established approach in lung cancer management with proven diagnostic, prognostic and predictive applications. It relies on detection of circulating tumor-derived nucleic acids present in plasma of the patient. In this study, a liquid biopsy approach was utilized to screen 118 consecutive lung cancer patients for four clinically-relevant variations in EGFR gene, which included three activating/sensitizing variations (Ex18 G719S, Ex19del E746-A750 and Ex21 L858R) and one acquired/resistance (Ex20 T790M, de novo) variation by droplet digital PCR, the most advanced third generation PCR technique. As expected, clinically-relevant EGFR variations were found in majority of the non-small cell lung cancer cases. However, among the handful of small cell lung cancer samples screened, sensitizing variations (Ex18 G719S and Ex21 L858R) were seen in almost all of them. Interestingly, Ex20 T790M variation was not detected in any of the cases screened.  The results of our study indicate that EGFR variations are present in SCLCs and highly sensitive liquid biopsy techniques like ddPCR can be effectively utilized for this purpose of screening EGFR variations in such samples.

Imaging Biomarkers and Liquid Biopsy in Assessment of Cervical Cancer

ABSTRACT

The role of imaging has been increasing in pretherapy planning and response assessment in cervical cancer, particularly in high-resource settings that provide access to computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET). In 2018, imaging was incorporated into the International Federation of Gynecology and Obstetrics staging system for cervical cancer. Magnetic resonance imaging is advantageous over CT for evaluation of the primary cervical cancer size and extent, because of superior contrast resolution. Furthermore, quantitative methods, including diffusion-weighted and dynamic contrast-enhanced MRI, show promise in improving treatment response and prognosis evaluation. Molecular imaging with fluorodeoxyglucose-PET/CT and PET/MRI can be particularly helpful in the detection of nodal disease and distant metastases. Semiautomated delineation of 3-dimensional tumor regions of interest has facilitated the development of novel PET-derived biomarkers that include metabolic volume and radiomics textural analysis features for prediction of outcomes. However, posttreatment inflammatory changes can be a confounder and lymph node evaluation is challenging, even with the use of PET/CT. Liquid biopsy has emerged as a promising tool that may be able to overcome some of the drawbacks inherent with imaging, such as limited ability to detect microscopic metastases or to distinguish between postchemoradiotherapy changes and residual tumor. Preliminary evidence suggests that liquid biopsy may be able to identify cervical cancer treatment response and resistance earlier than traditional methods. Future work should prioritize how to best synergize imaging and liquid biopsy as an integrated approach for optimal cervical cancer management.

Elevated serum CEA is associated with liver metastasis and distinctive circulating tumor DNA alterations in patients with castration-resistant prostate cancer

BACKGROUND

Elevated serum carcinoembryonic antigen (CEA) is used to identify "treatment emergent" forms of castration-resistant prostate cancer (CRPC) such as aggressive variant prostate cancer (AVPC). However, its individual utility as a prognostic marker and the genetic alterations associated with its expression have not been extensively studied in CRPC.

METHODS

This study retrospectively analyzed clinical outcomes and circulating tumor DNA profiles in 163 patients with CRPC and elevated or normal serum CEA. These same patients were then classified as AVPC or non-AVPC and compared to determine the uniqueness of CEA-associated gene alterations.

RESULTS

Patients with elevated CEA demonstrated higher rates of liver metastasis (37.5% vs. 19.1%, p = 0.02) and decreased median overall survival from CRPC diagnosis (28.7 vs. 73.2 mo, p < 0.0001). In addition, patients with elevated CEA were more likely to harbor copy number amplifications (CNAs) in AR, PIK3CA, MYC, BRAF, CDK6, MET, CCNE1, KIT, RAF1, and KRAS. Based on variant allele frequency we also defined "clonal" single-nucleotide variants (SNVs) thought to be driving disease progression in each patient and found that CEA expression was negatively correlated with clonal AR SNVs and positively correlated with clonal TP53 SNVs. Of these genetic associations, only the increases in clonal TP53 SNVs and KRAS amplifications were recapitulated among patients with AVPC when compared to patients without AVPC.

CONCLUSIONS

Together these findings suggest that CEA expression in CRPC is associated with aggressive clinical behavior and gene alterations distinct from those in AVPC.

Liquid biopsy for the assessment of adrenal cancer heterogeneity: where do we stand?

Almost 10 years have passed since the first attempts of liquid biopsy aimed at the characterisation of tumor cells present in the bloodstream from a regular sample of peripheral blood were performed. Liquid biopsy has been used to characterise tumor heterogeneity in various types of solid tumors including adrenocortical carcinoma. The development of molecular biology, genetics, and methodological advances such as digital PCR and next-generation sequencing allowed us to use besides circulating tumor cells a variety of circulating cell-free nucleic acids, DNAs, RNAs and microRNAs secreted by tumors into blood and other body fluids as specific molecular markers. These markers are used for diagnosis, to check tumor development, selecting efficient therapies, therapy monitoring and even possess prognostic power. In adrenocortical carcinoma, there are some studies reporting analysis of circulating tumor cells, circulating cell free DNA and microRNAs for assessing tumor heterogeneity. Among microRNAs, hsa-miR-483-5p seems to be the most important player. Combined with other microRNAs like hsa-miR-195, their expression correlates with recurrence-free survival. Most studies support the applicability of liquid biopsy for assessing temporal tumor heterogeneity (i.e. tumor progression) in adrenocortical cancer. In this mini-review, the available findings of liquid biopsy for assessing tumor heterogeneity in adrenocortical cancer are presented.

Microfluidics-Based Urine Biopsy for Cancer Diagnosis: Recent Advances and Future Trends

Urine biopsy, allowing for the detection, analysis and monitoring of numerous cancer-associated urinary biomarkers to provide insights into cancer occurrence, progression and metastasis, has emerged as an attractive liquid biopsy strategy with enormous advantages over traditional tissue biopsy, such as noninvasiveness, large sample volume, and simple sampling operation. Microfluidics enables precise manipulation of fluids in a tiny chip and exhibits outstanding performance in urine biopsy owing to its minimization, low cost, high integration, high throughput and low sample consumption. Herein, we review recent advances in microfluidic techniques employed in urine biopsy for cancer detection. After briefly summarizing the major urinary biomarkers used for cancer diagnosis, we provide an overview of the typical microfluidic techniques utilized to develop urine biopsy devices. Some prospects along with the major challenges to be addressed for the future of microfluidic-based urine biopsy are also discussed.

Updated Neoadjuvant Treatment Landscape for Early Triple Negative Breast Cancer: Immunotherapy, Potential Predictive Biomarkers, and Novel Agents

Simple Summary

In recent years, several agents have been tested in randomized clinical trials in addition to anthracycline and taxane-based neoadjuvant chemotherapy (NACT) in early-stage triple-negative breast cancer (TNBC) to improve pathological complete response rate and, ultimately, survival outcome. Platinum agents, immune checkpoint inhibitors (ICIs), and PARP-inhibitors are the most extensively studied, while established predictors of their efficacy are lacking. Based on the biological features of TNBC, the purpose of this review is to provide an overview of the role of platinum agents, immunotherapy, and novel target therapies in the neoadjuvant setting. Moreover, based on safety issues and financial costs, we provide an overview of potential biomarkers associated with increased likelihood of benefit from the addition of platinum, ICIs, and novel target therapies to NACT.

Abstract

Triple-negative breast cancer (TNBC) is characterized by the absence of hormone receptor and HER2 expression, and therefore a lack of therapeutic targets. Anthracyclines and taxane-based neoadjuvant chemotherapy have historically been the cornerstone of treatment of early TNBC. However, genomic and transcriptomic analyses have suggested that TNBCs include various subtypes, characterized by peculiar genomic drivers and potential therapeutic targets. Therefore, several efforts have been made to expand the therapeutic landscape of early TNBC, leading to the introduction of platinum and immunomodulatory agents into the neoadjuvant setting. This review provides a comprehensive overview of the currently available evidence regarding platinum agents and immune-checkpoint-inhibitors for the neoadjuvant treatment of TNBC, as well as the novel target therapies that are currently being evaluated in this setting. Taking into account the economic issues and the side effects of the expanding therapeutic options, we focus on the potential efficacy biomarkers of the emerging therapies, in order to select the best therapeutic strategy for each specific patient.

Making the Rounds: Exploring the Role of Circulating Tumor DNA (ctDNA) in Non-Small Cell Lung Cancer

Advancements in the clinical practice of non-small cell lung cancer (NSCLC) are shifting treatment paradigms towards increasingly personalized approaches. Liquid biopsies using various circulating analytes provide minimally invasive methods of sampling the molecular content within tumor cells. Plasma-derived circulating tumor DNA (ctDNA), the tumor-derived component of cell-free DNA (cfDNA), is the most extensively studied analyte and has a growing list of applications in the clinical management of NSCLC. As an alternative to tumor genotyping, the assessment of oncogenic driver alterations by ctDNA has become an accepted companion diagnostic via both single-gene polymerase chain reactions (PCR) and next-generation sequencing (NGS) for advanced NSCLC. ctDNA technologies have also shown the ability to detect the emerging mechanisms of acquired resistance that evolve after targeted therapy. Furthermore, the detection of minimal residual disease (MRD) by ctDNA for patients with NSCLC after curative-intent treatment may serve as a prognostic and potentially predictive biomarker for recurrence and response to therapy, respectively. Finally, ctDNA analysis via mutational, methylation, and/or fragmentation multi-omic profiling offers the potential for improving early lung cancer detection. In this review, we discuss the role of ctDNA in each of these capacities, namely, for molecular profiling, treatment response monitoring, MRD detection, and early cancer detection of NSCLC.

Ultra Deep Sequencing of Circulating Cell-Free DNA as a Potential Tool for Hepatocellular Carcinoma Management

BACKGROUND

Cell-free DNA (cfDNA) concentrations have been described to be inversely correlated with prognosis in cancer. Mutations in HCC-associated driver genes in cfDNA have been reported, but their relation with patient's outcome has not been described. Our aim was to elucidate whether mutations found in cfDNA could be representative from those present in HCC tissue, providing the rationale to use the cfDNA to monitor HCC.

METHODS

Tumoral tissue, paired nontumor adjacent tissue and blood samples were collected from 30 HCC patients undergoing curative therapies. Deep sequencing targeting HCC driver genes was performed.

RESULTS

Patients with more than 2 ng/µL of cfDNA at diagnosis had higher mortality (mean OS 24.6 vs. 31.87 months, p = 0.01) (AUC = 0.782). Subjects who died during follow-up, had a significantly higher number of mutated genes (p = 0.015) and number of mutations (p = 0.015) on cfDNA. Number of mutated genes (p = 0.001), detected mutations (p = 0.001) in cfDNA and ratio (number of mutations/cfDNA) (p = 0.003) were significantly associated with recurrence. However, patients with a ratio (number of mutations/cfDNA) above 6 (long-rank p = 0.0003) presented a higher risk of recurrence than those with a ratio under 6. Detection of more than four mutations in cfDNA correlated with higher risk of death (long-rank p = 0.042).

CONCLUSIONS

In summary, cfDNA and detection of prevalent HCC mutations could have prognostic implications in early-stage HCC patients.

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.

Clinical Validation of Companion Diagnostics for the Selection of Patients with Non-Small Cell Lung Cancer Tumors Harboring Epidermal Growth Factor Receptor Exon 20 Insertion Mutations for Treatment with Amivantamab

Amivantamab, an epidermal growth factor receptor (EGFR)-c-Met bispecific antibody, targets activating/resistance EGFR mutations and MET mutations/amplifications. In the ongoing CHRYSALIS study (ClinicalTrials.gov identifier NCT02609776), amivantamab demonstrated antitumor activity in patients with non-small cell lung cancer harboring EGFR exon 20 insertion mutations (ex20ins) that progressed on or after platinum-based chemotherapy, a population in which amivantamab use has been approved by the US Food and Drug Administration. This bridging study clinically validated two novel candidate companion diagnostics (CDx) tools for use in detecting EGFR ex20ins in plasma and tumor tissue, Guardant360 CDx and Oncomine Dx Target Test (ODxT), respectively. From the 81 patients in the CHRYSALIS efficacy population, 78 plasma and 51 tissue samples were tested. Guardant360 identified 62 positive (16 negative), and ODxT identified 39 positive (3 negative), samples with EGFR ex20ins. Baseline demographic and clinical characteristics were similar between the CHRYSALIS, Guardant360, and ODxT-identified populations. Agreement with local PCR/next-generation sequencing tests used for enrollment into CHRYSALIS demonstrated high adjusted negative (99.6% and 99.9%) and positive (100% for both) predictive values with the Guardant360 CDx and ODxT tests, respectively. Overall response rates were comparable between the CHRYSALIS, Guardant360 CDx, and ODxT populations. Both the plasma- and tissue-based diagnostic tests provided accurate, comprehensive, and complementary approaches to identifying patients with EGFR ex20ins who could benefit from amivantamab therapy.

The potential of cell-free and exosomal microRNAs as biomarkers in liquid biopsy in patients with prostate cancer

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.