Liquid Biopsy Analysis for Glioma Diagnosis: History
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Subjects: Neurosciences
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Gliomas are the most common primary tumors within the central nervous system (CNS), known for their significant genetic and epigenetic diversity, difficulties in monitoring, and elevated rates of relapse and mortality. Traditional tissue biopsy has long been the standard method for collecting and analyzing tumor cells, facilitating diagnosis, categorization of tumor subtypes, and prognosis prediction when the tumor's location is confirmed for surgical removal. Nonetheless, this approach is invasive and often challenging, making it unsuitable for routine patient screening, mutation detection, disease monitoring, or therapy resistance assessment. Consequently, a minimally invasive alternative known as liquid biopsy has emerged, providing a simpler means of tumor sampling and continuous monitoring. Liquid biopsy is increasingly recognized as an innovative and preferred method for obtaining rapid insights into potential tumor risk, personalized diagnosis, prognosis, and recurrence assessment.

  • glioma
  • glioblastoma
  • tissue biopsy
  • liquid biopsy
  • cfDNA
  • circulating tumor cells
  • exosomes
  • LINE-1
  • epigenetics
  • radiogenomics

1. Introduction

Gliomas comprise the most frequent primary tumor of the central nervous system (CNS), characterized by increased heterogeneity and aggressiveness, as well as high relapse and mortality rates [1]. More specifically, gliomas are responsible for 24.7% and 74.6% of all primary and malignant brain tumors, respectively [2]. Glioblastoma (GB), the most malignant glioma subtype is a highly aggressive, infiltrating, and poorly managed brain tumor. Currently available therapeutical approaches include surgical resection, followed by radiotherapy, as well as temozolomide (TMZ) chemotherapy. Thus far, limited drug penetration to the CNS, along with the rapid development of chemotherapy resistance, present ongoing challenging issues that contribute to poor prognosis [3,4].
Until now, tissue sample acquisitions from biopsies have been used for histological and molecular tumor analysis to confirm diagnosis, classify tumor types, detect tumor-specific mutations, and guide therapeutic protocols [5]. Tissue biopsy, although of major importance, is, however, an invasive and oftentimes challenging procedure. A surgical brain tissue biopsy increases the risk of bleeding and the likelihood of damaging an important brain area (e.g., glioma infiltrating a sensitive area of the frontal lobe), which can lead to neurological deficits, especially in the cases of the developing pediatric brain [6].
Moreover, invasive procedures are characterized by limitations in acquiring tumor samples in both efficient quantity and quality of tumor material. Sequential collection of tissue biopsies during treatment to monitor tumor response and relapse also poses a major challenge in tumor profiling [7]. It often provides limited material to perform all necessary molecular tests that are required to achieve a reliable diagnosis. In this context, the detection of mutations, genetic and epigenetic defects, or polymorphisms is not always possible.
In addition, tissue biopsy may not enable satisfactory detection of early-stage tumor or residual lesions and is not suitable for screening [8]. Furthermore, temporal and spatial tumor heterogeneity may decrease the practical utility of tissue biopsies to be used as tools for monitoring tumor progression and evaluating response to therapy [5]. In multifocal cases in particular, multiple biopsies may be necessary in order to obtain an accurate representation of the tumor, since invasive tumors constantly evolve both spatially and temporally over time or in response to treatment [7].
To this end, the minimal invasive procedure of liquid biopsy has surfaced as a solution to these issues, constantly progressing to enable first tumor diagnosis and collecting information on risk, prognosis, and recurrence potential.

2. Basic Principles and Applications of Liquid Biopsy

Tumor cells may release multiple components into the circulation that can travel to distant organs throughout the body. These may include intact cancer cells and also tumor cell DNA and RNA, proteins, or exosomes that can be exploited as blood-circulating cancer biomarkers and may provide us with similar information to that of tissue biopsy, pinpointing the primary origin site and playing a key role in routine monitoring of tumor progression or treatment efficacy [5].
Given the increasing sensitivity of techniques that are used to study nucleic acids, it is nowadays possible to analyze tumor-released nucleic acids and blood-circulating cells. Genomic and epigenomic analysis of the circulating tumor DNA, for example, is an important novel tool regarding treatment. By using liquid biopsy (LB), clinicians can obtain data related to risk and disease prognosis and can predict chances of recurrence [9]. In more detail, LB is a minimally invasive procedure (e.g., venipuncture) that enables detection of several different analytes [6] in a variety of biological fluids to monitor disease progression [10,11]. Since most tumors encounter blood circulation, LB usually involves blood sampling. However, other body fluids, such as mucosa, fluid from pleural effusions, cerebrospinal fluid (CSF), and urine, may also be analyzed [12,13].

2.1. Analytes Detected in Biofluids by Liquid Biopsy

In 1996, the National Comprehensive Cancer Network (NCCN) introduced several biomarkers into clinical practice, based on clinical and/or technical factors for diagnostic and prognostic purposes [14]. More recently, in 2011, the NCCN updated and established specific biomarkers as standard of care in some cancer types, including gliomas [15]. Analytes with a biomarker potential that can be detected through LB include cell-free DNA (cfDNA), cell-free RNA (cfRNA) and circulating proteins, circulating tumor cells (CTCs), and extracellular vesicles (EVs) such as exosomes, which can encapsule tumor DNA and other nanomolecules, such as mRNAs/miRNAs (Figure 1) [16,17].
Figure 1. Detection of various tumor analytes in a variety of biofluids (CSF, urine, blood) with liquid biopsy. Several types of biofluids can be collected by using liquid biopsy and tumor-derived analytes (cfDNA, cfRNA, exosomes) measured using genomic processes to aid in tumor diagnosis, prognosis, and monitoring response to therapy (created with BioRender access on 24 June 2023).

3. Biomarkers Detected through Liquid Biopsy Analysis for the Diagnosis of Gliomas

The ability of a liquid biopsy to analyze tumor products that are found in body fluids has led to its increasing utilization in different types of tumors. This technique provides vital diagnostic and prognostic information, as well as real-time updates on tumor status. In the case of gliomas, the use of a liquid biopsy is extremely promising [74].

3.1. cfDNA, cfRNA, and Circulating Proteins in the Diagnosis of Gliomas

3.1.1. cfDNA

LB has allowed the detection of cfDNA in cancer patients, as mentioned above, which has created the potential of its incorporation into clinical practice, with the goal of identifying both genetic and epigenetic alterations in tumors. cfDNA may be a suitable molecular marker, indicative of tumor status, which will enable disease monitoring and distinction between tumor-free individuals and brain tumor patients [75].
One study demonstrated that the serum of control subjects was consistently characterized by low levels of cfDNA, in contrast to GB patients who had higher cfDNA concentrations. This may suggest that cfDNA could serve as a useful biomarker for differentiating GB patients from healthy individuals and serve as an indicator for tumor progression [20].
cfDNA may also help in the quantitative measurement of genetic (e.g., IDH mutations) or epigenetic (MGMT methylation) alterations [75,76]. In the cfDNA derived from glioma patients, there are various genes and epigenetic alterations that can be detected and used as biomarkers to diagnose/monitor the disease. A prominent example is the H3K27M mutation characteristic of diffuse midline gliomas (DMG). In the study of Daphne Li et al., cfDNA was obtained from two types of specimens: H3.3K27M mutant and H3 wildtype (H3WT). The specimens included H3.3K27M tumor tissues (four samples), CSF (six samples), plasma (four samples), and human primary pediatric glioma cells. The researchers observed a sensitivity and specificity of 100% in detecting mutations in both matched DMG tissue and CSF samples [77]. Another study demonstrated that H3K27M was detected in the CSF and plasma of 88% of patients with DMG. Among the two, CSF exhibited the highest concentration of ctDNA [78].
Global DNA methylation (LINE-1 or L1) may also play a pivotal role in the epigenetic status of glioma cells, enabling diagnosis through cfDNA analysis. The addition of a methyl group to cytosine, leading to the formation of 5-methylcytosine, is the most well-known mechanism of DNA modification through epigenetic processes, playing a significant role in the development and progression of cancer and, specifically, of gliomas [79,80]. The dysregulation of cells at a systemic level, often associated with tumor development, can result from either DNA hypomethylation or increased activity of LINE-1 transposons [81]. The majority of transposition events occurring in the human genome are carried out by non-LTR (long-terminal repeat) retrotransposons, with long interspersed elements (LINEs) being the most prevalent. Of all LINEs, LINE-1 accounts for approximately one-sixth of genomic transposition and exists as multiple copies in cell-free blood samples. Due to its abundance and unique characteristics, such as methylation status, it has the potential to serve as a valuable epigenetic biomarker for tumor detection in liquid biopsy samples [79].

3.1.2. cfRNA

When it comes to cfRNAs and their use in gliomas, Dong et al. discovered that the serum of GB patients exhibited a significant decrease in 24 miRNAs and a substantial increase in 115 miRNAs, which was not observed in the serum of healthy controls [93]. Furthermore, Wang et al. identified three downregulated miRNAs, namely miR-128, miR-485-3p, and miR-342-3p, in patients compared with controls. These miRNAs demonstrated a correlation with GB grades and served as biomarkers for assessing tumor grading and monitoring treatment response [94].
MicroRNA-21 is the most extensively studied miRNA in cancer and its overexpression has been consistently observed both in tissue and plasma of GB patients. This elevated expression is closely linked to lower overall survival rates and higher tumor grading [95]. miR-21 functions as an anti-apoptotic factor in glioblastoma cell lines by exerting its effects through caspase inhibition. The suppression of miR-21 activity consequently impedes cell growth, enhances apoptosis, and diminishes the proliferation of GB cancer cells [95,96].
It is worth noting a study that identified TP73-AS1 as a clinically relevant long non-coding RNA (lncRNA) in GB. The researchers observed a significant upregulation of TP73-AS1 in primary GB samples. They provided evidence that TP73-AS1 serves as a robust prognostic biomarker, as this lncRNA promotes tumor aggressiveness and confers resistance to TMZ treatment in GB cancer stem cells [97].

3.1.3. Circulating Proteins

Given the remarkable patient and disease heterogeneity, as well as the broad protein involvement in multiple processes, it is difficult to find diagnostic plasma/serum markers for glioblastoma with sufficient clinical value. However, extensive research has identified the levels of several circulating proteins to be associated with the presence of GB. One example is the plasma glycoprotein, haptoglobin, which is an acute phase protein involved in the protection of tissue damage and oxidative stress [100]. Haptoglobin’s levels change during pathologies and, although its single estimation may not be specific and sensitive enough, several proteoforms of haptoglobin (α2 and β-chain) have been detected upregulated in GB patients’ plasma, indicating its potential use as a GB-specific blood biomarker [100].
In addition, a quantitative proteomic analysis showed that several plasma proteins, such as carnosinase 1 (CNDP1) that regulates carnosine levels, the inflammatory marker ferritin light chain (FTL), and the Ca2+ signaling protein S100A9, were found to be altered in GB tissues, with CNDP1 been suggested as a potential drug target. This confirms that plasma-based tests for initial diagnosis or recurrence monitoring can be highly useful for GB [101,102]. Moreover, the study of Pérez-Larraya et al. performed a comprehensive analysis of insulin-like growth factor binding protein 2 (IGFBP-2), the intermediate filament (IF) III protein GFAP, and the glycoprotein YKL-40 plasma levels as a supplementary diagnostic and prognostic tool [103]. This approach holds great promise, particularly for patients with inoperable brain lesions [103]. Interestingly, the presence of the glycoprotein’s fetuin-A auto-antibodies was also revealed as indicators of GB development [104]. Ectopic fetuin-A levels have been suggested to play a role in tumor progression, including GB. Therefore, evaluation of fetuin-A auto-antibodies in the serum of GB patients was proposed to potentially serve as a screening tool, presenting one of the earliest indicators for GB growth [104].

3.2. CTCs in Glioma Diagnosis

Numerous studies have confirmed the significant role of CTCs in CNS tumors. CTCs provide a less invasive way of obtaining tumor samples for cancer detection; certain CTC genotypes may indicate primary tumor progression and changes in malignant genetic information during disease relapse. GB has been reported to have a high prevalence of CTCs, which is estimated to be around 75% [108].
CTC concentrations have been utilized for the detection of various conditions. According to Santos et al., CTCs exhibit promising results in the early detection of colorectal cancer as they can be identified in the blood of patients who have recently developed the disease. As a result, CTC testing could be utilized to diagnose colorectal cancer [109].
When it comes to gliomas, the blood brain barrier (BBB) may restrict the quantity of CTCs which are found in the bloodstream. Despite this, circulating cells have been identified in glioma patients’ blood and several studies have reported the detection of CTCs in the bloodstream of glioma patients through the use of various isolation techniques. After using the technology of CTC-iChip to enrich CTCs and staining them with antibodies, such as SOX2, EGFR, tubulin b-3, c-MET, and A2B5, Sullivan et al. identified CTCs in GB patients’ blood with a frequency of 39%. They also discovered that the CTCs exhibited a mesenchymal molecular signature [48]. Muller et al. conducted a study where they employed Ficoll–Paque gradients through differential centrifugation, followed by GFAP staining, to identify 20.6% of CTCs [108]. In addition, Gao et al. demonstrated that CTCs were present in 77% of blood samples from patients with brain cancer and in 82% of patients with GB [52].
An interesting study by MacArthur et al. suggested that CTCs could also serve as a prognostic factor. Using density gradient centrifugation, they isolated CTCs and analyzed the activity of the telomerase enzyme in brain cancer patients. The study revealed that before radiotherapy treatment, CTCs were isolated in 72% of patients versus only in 8% after treatment [70]. Moreover, the anti-glioma aptamers Gli-233 and Gli-55 have been used to detect CTCs in LBs in order to increase diagnostic specificity [110]. Aptamers are nucleic acid molecules that bind exclusively to their targets, such as cancer-related proteins, with high affinity and selectivity [111]. They have therefore already been used in biosensing, bioregulation, and bioimaging as reliable recognition ligands [112]. Kichkailo et al. also demonstrated that aptamers may specifically bind to glial tumor cells for CNS tumor detection [110]. Although more research is necessary to uncover the full potential of CTCs in diagnosing gliomas and GB, their use as prognostic factors for gliomas is very promising.

3.3. Exosomes in Glioma Diagnosis

Another important characteristic of GB cells is their ability to use invadopodia, through which they are capable of invading adjacent cells, specifically astrocytes. Invadopodia are GB cell membrane-derived extensions that adhere to neighboring tissues and promote the proteolytical degradation of the matrix, thus allowing invasion [113,114]. Several proteins excreted from GB-derived exosomes are linked to invadopodia biogenesis and subsequently GB-invasive potential, among which are annexin A1 (ANXA1), actin-related protein 3 (ACTR3), integrin β1 (ITGB1), calreticulin (CALR), and programmed cell death 6-interacting protein (PDCD6IP) [114]. Hallal et al. also observed the formation of podosomes in astrocytes and degradation of the matrix after their interaction with exosomes derived from GB cells, a process that appears to be favored by decreased p53 levels. Exosomes thereby exhibit carcinogenic potential and promote the neighboring astrocytes to become tumorigenic [115].
In this context, GB exosomes can be detected both in the blood and the CSF by using the minimally invasive technique of liquid biopsy. A robust number of tumor-derived exosomes may be found in the CSF. It is important to note that CSF is not contaminated with blood-related EVs, for example, platelet-derived exosomes. However, on the other hand, blood samples are more conveniently and less invasively collected compared with the CSF [113,116].
Furthermore, Shao et al. described how a nuclear magnetic resonance system can detect GB-expelled microvesicles in blood samples [117]. Studies have shown that exosome-carried molecules may promote tumor development and therapy resistance through the formation of a tumor-friendly microenvironment. Therefore, exosomes have been suggested as promising tools in GB diagnosis and prognosis, enabling a more specific characterization of the tumor [118,119].
Despite being carriers of many miRNA types, including miR-21/-29a/-221/-222, etc., as demonstrated in several studies (in vitro and microarray analyses), exosomes also play a key role in boosting proliferation and inhibiting GB cell apoptosis [58,120]. They could therefore be utilized as a promising delivery vehicle for tumor-suppressive miRNAs that target gliomas [121]. Approximately 1000 proteins have been identified in GB exosomes using mass spectrometry analysis; they mostly act as pro-angiogenic factors in normal endothelial cells of the brain, such as angiogenin, IL-6/-8, and tissue inhibitor of metalloproteinase-1 and 2 (TIMP-1, and TIMP-2), capable of promoting malignancy by causing hypoxia [122,123].
Exosomes may also transfer receptors with tumorigenic features, such as epidermal growth factor receptor vIII (EGFRvIII), human epidermal growth factor receptor 2 (HER2), and platelet-derived growth factor (PDGFR), which promote GB proliferation to healthy stromal cells [123]. Furthermore, exosomes deliver phosphatase and tensin homolog (PTEN), which is present in the nucleus or cytoplasm and whose absence has been associated with tumorigenesis [124]. Ndfifip1 protein plays a major role in exosome internalization. Interestingly, the Ndfifip1 protein is repressed in GB; subsequently, the intranuclear concentration of PTEN is also suppressed, allowing tumor cells to proliferate and survive [124].

4. Combination of Radiogenomics and Liquid Biopsy for Glioma Diagnosis

Radiogenomics is a field that integrates large amounts of quantitative data obtained from medical images with individual genomic phenotypes and uses deep learning techniques to develop a predictive model. This model is useful for stratifying patients, guiding therapeutic strategies, and assessing clinical outcomes [140].
The combination of liquid biopsy and radiomics/radiogenomics can offer a promising avenue for non-invasive disease diagnosis and provide valuable insights for treatment planning (Figure 2). Both approaches have individually shown great potential, but their combination can lead to even more accurate and comprehensive diagnoses. The study of images using artificial intelligence (AI) and machine and deep learning techniques has progressed significantly in recent years. These methods involve an increasingly complex analysis of computational processes and imaging features, with the potential to accurately predict the molecular alterations necessary for correct disease diagnosis. As a result, they represent a promising approach for improving the accuracy and precision of glioma diagnosis [141,142]. In more detail, the field of radiogenomics offers a unique opportunity to predict genetic mutations, the status of molecular markers, and chromosomal aberrations through the analysis of imaging features. This approach utilizes imaging data as a substitute for the presence of genetic alterations, providing a non-invasive and efficient way of diagnosing and monitoring gliomas [143].
Figure 2. Impact of radiogenomics on diagnosis of brain tumors. Radiogenomics integrates large amounts of quantitative data obtained from medical images with individual genomic phenotypes from liquid biopsy analysis to enable efficient glioma diagnosis (created with BioRender, accessed 12 July 2023).
Radiogenomics has already been employed in other forms of cancer, such as breast [144] and lung cancer [145]. These studies have demonstrated the potential of radiogenomics to accurately predict the genetic characteristics of tumors through the analysis of imaging data. The extension of this approach to gliomas represents a significant opportunity to improve the accuracy and efficiency of non-invasive diagnosis and monitoring.
In the study of Li Y et al., for example, that used MRI radiomics (machine learning), the authors were able to predict ATRX mutations in low-grade gliomas [146]. In another study, the same mutations were identified in gliomas with deep learning, with 94% sensitivity and 92% specificity [147]. Diffuse midline gliomas with H3F3A histone mutations have greater enhancement in the T2 sequence, while tumors without the mutation have a poor identification of the non-contrast-enhancing tumor (NCET) margin. Furthermore, non-mutated tumors present with sound edema and cortical invasion [148]. A study of radiomics analysis (multiparameter MRI) managed to identify that tumors harboring TERT mutations have more necrotic areas, since TERT mutations suggest a high-grade profile [149].
Moon et al. also identified several characteristics of high-grade gliomas relative to MGMT promoter methylation [150]. When it comes to other brain tumors and, particularly, oligodendrogliomas, which are subcategorized to IDH-mutant and 1p/19q co-deleted [151], studies have been able to predict the 1p/19q codeletion with high specificity and sensitivity using, for example, a textural analysis of the T2 sequence [152,153,154]. It therefore becomes evident that the combination of liquid biopsy with the genomics component of radiogenomics profiling represents a promising approach to revolutionize cancer treatment. This combination may have the potential to facilitate early diagnosis, provide more accurate prognostic assessment, and enable real-time disease monitoring, all while minimizing invasiveness. Furthermore, this personalized approach to non-invasive brain tumor diagnosis could pave the way for precision medicine, tailored to the individual needs of each patient.

This entry is adapted from the peer-reviewed paper 10.3390/biomedicines11092371

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