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Das, S.; Dey, M.K.; Devireddy, R.; Gartia, M.R. Biomarkers in Cancer Detection, Diagnosis, and Prognosis. Encyclopedia. Available online: https://encyclopedia.pub/entry/53982 (accessed on 06 July 2024).
Das S, Dey MK, Devireddy R, Gartia MR. Biomarkers in Cancer Detection, Diagnosis, and Prognosis. Encyclopedia. Available at: https://encyclopedia.pub/entry/53982. Accessed July 06, 2024.
Das, Sreyashi, Mohan Kumar Dey, Ram Devireddy, Manas Ranjan Gartia. "Biomarkers in Cancer Detection, Diagnosis, and Prognosis" Encyclopedia, https://encyclopedia.pub/entry/53982 (accessed July 06, 2024).
Das, S., Dey, M.K., Devireddy, R., & Gartia, M.R. (2024, January 17). Biomarkers in Cancer Detection, Diagnosis, and Prognosis. In Encyclopedia. https://encyclopedia.pub/entry/53982
Das, Sreyashi, et al. "Biomarkers in Cancer Detection, Diagnosis, and Prognosis." Encyclopedia. Web. 17 January, 2024.
Biomarkers in Cancer Detection, Diagnosis, and Prognosis
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Biomarkers are vital in healthcare as they provide valuable insights into disease diagnosis, prognosis, treatment response, and personalized medicine. They serve as objective indicators, enabling early detection and intervention, leading to improved patient outcomes and reduced costs. Biomarkers also guide treatment decisions by predicting disease outcomes and facilitating individualized treatment plans. They play a role in monitoring disease progression, adjusting treatments, and detecting early signs of recurrence. 

biomarkers DNA RNA cancer

1. Introduction

A biomarker is a biological phenomenon that can be difficult to find, yet indicates a clinically significant outcome or interim consequence. Biomarker applications include identifying, characterizing, and monitoring diseases. Additionally, biomarkers can act as prognostic indicators, inform individualized treatment plans, and anticipate and manage negative medication reactions. Understanding the fundamental link between a biomarker and its clinical result is crucial for adequately appreciating its significance [1].
Cancer is an intricate condition marked by genetic and epigenetic changes that throw off the balance between cellular development and cell death. It is a major global health issue that kills many people every year worldwide [2]. Significant molecular and tissue alterations are required for cancer growth. Invaluable clinical data in the form of biomarkers can be generated by analyzing biomolecules such as nucleic acids, carbohydrates, proteins, lipids, and metabolites linked to cancer development [3]. Early detection plays a crucial role in minimizing the morbidity and mortality associated with cancer. Therefore, there is an urgent need for genuine and reliable cancer indicators. Prostate-Specific Antigen (PSA), Carcinoembryonic Antigen (CEA), and CA-125/MUC16 are frequently used cancer indicators, while exosomes, microRNA, and circulating tumor cells are emerging as a new source of biomarkers [4].

2. Challenges Associated with Detecting Early-Stage Tumors

Successful cancer treatment depends on early detection [5]. Yet, physiological and mass transport barriers restrict the amount of biological indicators that can be released from early lesions [6][7].
Finding intrinsic biomarkers through blood and biofluid examination is the primary objective of ongoing research. To improve specificity, bioengineered sensors and synthetic markers are being developed. Imaging systems also aid in detecting and localizing tumors [8][9][10]. The typical spatial resolution of a positron emission tomography (PET) scanner is about 1 cm3, and hence, very small tumors (diameter < 5 mm) will be missed by the PET imagers. The typical blood draw is 5–10 mL, which is three orders of magnitude (1/1000th) smaller than the body’s total blood volume (~5 L). This means that the biomarkers shed by the tumor will be diluted > 1000 times when it is detected (Figure 1). Further, there are challenges in detecting genomic materials. For example, circulating tumor DNA (ctDNA) has a half-life of ~1.5 h. So, in a 24 h time period, it will undergo 16 half-lives. This means that by the time it is detected, only 0.0015% of the original materials will remain [9][10][11][12]. A potential ten-year window for early cancer detection is suggested by multicompartment models and studies on the genomic timeline. However, current screening techniques can find cancers that have been present for ten years or longer and are indolent. Cancers that spread quickly and aggressively and have poor clinical outcomes include triple-negative breast cancer and high-grade serous ovarian carcinoma. These problems are intended to be solved by activity-based or genetically encoded mechanisms for early detection in synthetic biomarker research.
Figure 1. Difficulties related to the identification of tumors in their early stages. Due to their tiny size and the difficulties in transferring biomarkers from the tumor microenvironment to the bloodstream, early-stage cancers are challenging to detect. This is brought on by difficulties with biomarker transfer, dilution, and the kidneys’ quick degradation and filtration processes. Only a few tumor-associated biomarkers can be found in a typical blood sample of 5–10 mL, which is a small part of the overall blood volume.

3. Biomarkers in Cancer Detection, Diagnosis, and Prognosis

3.1. Biofluid Biomarkers

Biofluids provide a way to quickly evaluate and track diseases [12]. Urine, saliva, blood, and sweat are examples of biofluids that contain important data regarding the disease under investigation. These biofluid specimens can be easily collected non-invasively and are ideal for clinical studies [13]. Each biofluid has unique advantages and challenges [14]. Saliva is readily available and includes electrolytes like sodium, potassium, calcium, magnesium, bicarbonate, and phosphates, whereas urine contains urea, chloride, sodium, and potassium salts. Sweat mainly contains sodium, chloride, minerals, lactic acid, and urea [15].
Cancer detection and tracking uses various biofluids, such as urine, saliva, blood, and cerebrospinal fluid (CSF) [16]. Studies have identified KRAS, MBD3L2, ACRV1, and DPM1 as biomarkers in salivary mRNA to detect pancreatic cancer with high specificity [17][18][19][20][21]. Salivary proteins with high specificity and sensitivity to identify lung cancer include calprotectin, AZGP1, and HP. Salivary DNA can also detect mutations in the genes PI3K, CDKN2A, FBXW7, HRAS, and KRAS in mouth and throat tumors [22][23][24][25][26].
There are various techniques to detect genomics (qPCR, RNA, and DNA sequencing), proteomics (mass spectrometry, ELISA, and Western blotting), and lipidomics (mass spectrometry) to find cancer biomarkers in biofluids. For protein extraction and separation, several methods are used, including surface-enhanced laser desorption/ionization (SELDI), 2-dimensional gel electrophoresis (2-DE), difference gel electrophoresis (2D-DIGE), and Liquid Chip. Mass spectrometry and bioinformatics are used to identify proteins, with Western blot and ELISA used to confirm the results. Sample variability, inter-laboratory analytical variability, and sample type selection are difficulties in biomarker discovery. Many studies have looked into finding cancer-associated hypermethylated DNA fragments in cancer patients’ circulating free DNA (cfDNA), especially in cases of gastric cancer (GC). A number of hypermethylated genes, including RPRM, XAF1, and a KCNA4 and CYP26B1 combination, have demonstrated high diagnostic value for GC detection. Before these assays can be used in clinical settings, a few technical issues must be resolved. The majority of studies employ sodium bisulfite treatment followed by methylation-specific PCR (MSP) or DNA sequencing, but these methods could produce false-positive results because unmethylated cytosine residues are not completely converted.

3.2. Imaging Biomarkers

Tumor, node, metastasis (TNM) staging, objective response, and left ventricular ejection fraction are just a few of the imaging biomarkers (IBs) that are critical for clinical oncology [27]. Cancer research frequently uses imaging techniques like computed tomography (CT), magnetic resonance imaging (MRI), positron emission tomography (PET), and ultrasonography. New IBs need to be validated and qualified in order to fill in the translational gaps [28]. A total of 14 important recommendations have been made by Cancer Research UK (CRUK) and the European Organization for Research and Treatment of Cancer (EORTC) to hasten the clinical translation of IBs [29][30][31]. These suggestions for achieving IB qualification emphasize parallel validation procedures, cost-effectiveness analysis, standardization, accreditation systems, precision evaluation, alternative validation frameworks, and multicenter studies [32][33][34][35][36][37].
IBs are derived from medical images. They offer non-invasive, cost-effective screening, tumor detection, patient progress, and therapy response monitoring tools [38]. Staging systems document the existence, dimensions, and quantity of abnormalities in tumor, lymph node, and additional metastatic locations to establish a structured categorical indicator of the patient’s disease severity. IBs have the ability to map tumor heterogeneity, monitor changes in tumors over time, and assess a person’s multiple lesions [39][40][41].
The evaluation of lesions at tumor, nodal, and metastatic sites using staging systems is crucial for the diagnosis and prognosis of cancer. The American Joint Committee on Cancer (AJCC) offers recommendations for precise and consistent reporting in radiology. TNM staging is frequently used and has prognostic value for a variety of cancer types. It is based on imaging modalities like CT, MRI, SPECT, and PET. TNM staging can occasionally be used to forecast treatment outcomes.

3.3. Needle Biopsy

Imaging tests are essential in identifying and tracking cancer [42]. These examinations use various forms of energy, such as X-rays, sound waves, radioactive particles, or magnetic fields, to produce finely detailed images that reveal important details about the structure and location of the tumor [43][44][45][46]. It is crucial to remember that imaging tests do have their limitations. They cannot identify specific cancer cells, and their results are inconclusive. Imaging tests are typically validated by biopsy [47].
A cancer biopsy is a test for diagnosis employed to identify the kind and properties of the tumor cells and confirm or rule out the existence of cancer. Findings are crucial for making additional medical choices (grading of tumor; chemotherapy vs. radiation vs. immunotherapy) [48][49][50][51]. In accordance with the precise spot and accessibility of the suspicious region, biopsies can be carried out using a variety of approaches (Figure 2), including surgical biopsies, endoscopic biopsies, and needle biopsies [52]. Needle biopsy may employ a larger needle for collecting large tissue specimens or a fine needle aspiration for gathering a small sample from cells and fluid. A special needle with a suction mechanism is used in vacuum-assisted biopsy for acquiring tissue specimens. These methods provide versatility in gathering appropriate samples for analysis [53][54].
Figure 2. Commonly used non-invasive techniques for examining biomarkers in solid tumors.

3.4. Tissue Imaging

Immunohistochemistry (IHC), an approach used for tissue image processing, allows researchers to analyze particular proteins or antigens in tissue samples. Antibodies designed to bind to specific protein targets in tissue sections are used in this procedure. A secondary antibody is coupled to a recognition molecule after the primary antibody is bound to its target. The results are visualized under a microscope. The results are typically in the form of an alteration in color or fluorescence, indicating the target protein’s existence and location. IHC is a widely used method in pathology studies and diagnostics that can reveal important details about the arrangement, expression levels, and localization of particular proteins in tissue specimens.

4. Types of Cancer Biomarkers

4.1. Genetic Biomarkers

4.1.1. Mutations and Gene Alterations

Mutations and gene alterations are important cancer biomarkers that can provide valuable information about the underlying genetic changes driving the development and progression of cancer. Here are some examples of mutation- and gene alteration-based cancer biomarkers. The BRAF V600E mutation activates cell growth, aiding targeted therapy selection in melanoma patients [55]. EGFR mutations (e.g., exon 19 deletions, L858R point mutation) increase sensitivity to EGFR inhibitors in non-small-cell lung cancer (NSCLC) [56]. In colorectal, KRAS mutations (30–40% cases) activate signaling pathways, affecting treatment response [57]. BRCA1/BRCA2 mutations increase cancer risk in breast/ovarian cancer, and guide therapy selection [58]. HER2 amplification/overexpression indicates aggressive behavior in breast/gastric cancer, and is generally treated with anti-HER2 antibodies [59]. IDH mutations affect cellular metabolism and serve as diagnostic and prognostic markers in glioma patients [60].

4.1.2. Gene Expression Profiles

Gene-expression-profile-based cancer biomarkers involve analyzing the patterns of gene expression in cancer cells to provide insights into tumor behavior, prognosis, and treatment response. Here are some examples of gene-expression-profile-based cancer biomarkers:
Oncotype DX in Breast Cancer: Oncotype DX is a genomic test that assesses the expression of a panel of about 16 genes involved in breast cancer. It provides a recurrence score (RS) that predicts the likelihood of disease recurrence and guides treatment decisions, particularly in early-stage hormone receptor-positive breast cancer. The genes in question are ERBB2 (also known as HER2), ESR1 (estrogen receptor 1), PGR (progesterone receptor), BIRC5 (survivin), SCUBE2 (signal peptide, CUB domain, EGF-like 2), STK15 (Aurora kinase A), BCL2 (B-cell lymphoma 2), MKI67 (Ki-67), GSTM1 (glutathione S-transferase mu 1), CD68 (cluster of differentiation 68), BAG1 (BCL2-associated athanogene 1), MMP11 (matrix metallopeptidase 11), CTSL2 (cathepsin L2), GRB7 (growth factor receptor-bound protein 7), GSTM1 (glutathione S-transferase mu 1), and CDKN1B (cyclin-dependent kinase inhibitor 1B) [61].
MammaPrint in Breast Cancer: MammaPrint is a gene-expression-based assay used to analyze the activity of a set of genes (~18 genes) in breast cancer. It provides a genomic risk score (RS) that helps determine the risk of distant metastasis and assists in treatment decision making, particularly in early-stage breast cancer. The list of genes includes AURKA (Aurora kinase A), BIRC5 (survivin), CCNB1 (cyclin B1), CDC2 (cell division cycle 2), CKS1B (CDC28 protein kinase regulatory subunit 1B), DLG7 (discs large homolog 7), ERBB2 (also known as HER2), ESR1 (estrogen receptor 1), FOXM1 (forkhead box M1), MMP11 (matrix metallopeptidase 11), MYBL2 (myb-related protein B), NDC80 (kinetochore protein NDC80 homolog), NEK2 (NIMA-related kinase 2), RACGAP1 (Rac GTPase-activating protein 1), RRM2 (ribonucleotide reductase M2 subunit), STK15 (Aurora kinase A), TYMS (thymidylate synthase), and UBE2C (ubiquitin-conjugating enzyme E2C) [62].

4.1.3. DNA as a Cancer Biomarker

The initial markers tested for tumor staging were circulating DNA, as shown in Figure 3. Elevated concentrations of serum DNA have been linked to cancer (most particularly, metastatic cancer). Oncogene alterations, mismatch-repair gene mutations, and mutations in tumor suppressor genes can all be used as DNA biomarkers. In over 50% of sporadic malignancies, mutations in the p53 tumor suppressor gene are found, and mutations in the KRAS oncogene indicate metastatic spread [55][56][57]. A TP53 mutation passed down through the generations (Li–Fraumeni syndrome) raises the likelihood of acquiring several of the same malignancies. Several genes have single nucleotide polymorphisms, including RAD1, CYP1A1, and BRCA1/2 (breast cancer), PGS2 (lung cancer), and XRCC1, p53, and ATM (lung, head, and neck cancers). Diagnosis has been associated with mutations in DNA nucleotides in tumor promoters such as APC, RAS, and tumor suppressor genes. Tissue, sputum, serum, saliva, cerebrospinal fluid (CSF), bronchial tear, tumor cells circulating in the bone marrow, and blood are all potential sources of DNA [63][64][65]. Mutations in mitochondrial DNA have been postulated as diagnostics biomarkers for various malignancies [63][66][67]. Haplotype analysis was used to investigate the mitochondrial inheritance pattern in cancer patients. Researchers used polymerase chain reaction to look for critical polymorphic locations in the mitochondrial DNA in specimens from cancer patients and healthy subjects to see if there is a link connecting mitochondrial genotype and cancer. Nine mitochondrial genomic haplogroups have been described, namely, H, I, J, K, T, U, V, W, and X. U is linked with a high chance of developing renal and prostate cancer among these haplogroups [63].
Figure 3. DNA from free cells and malignant cells in circulation. Circulating tumor cells (CTC) spread throughout the blood vessels after escaping from original locations and forming metastases in the distal organs. Dead cancer cells or expanding tumor cells release cell-free DNAs (cf-DNAs) into the bloodstream. RBC = red blood cell; WBC = white blood cell [68].

4.1.4. RNA as a Cancer Biomarker

Differential display, RT-qPCR, bead-based approaches, and micro-array analysis are among the techniques applied to diagnose potential biomarkers at the RNA expression level [69]. MicroRNAs (miRNAs) are short non-coding RNAs linked to clinical features in several cancers. The expression of particular miRNA populations is related to clinical features in a time- and tissue-dependent pattern [70][71][72]. To promote tumorigenesis, metastasis, immune evasion, and angiogenesis, microRNAs regulate the transcription of their target mRNAs [73][74]. Tumor microRNA profiles can be used to identify important subgroups, survival rates, and responsiveness to therapy.
Furthermore, cancer-associated microRNA markers may be detectable in bodily fluid, enabling individuals with cancer microRNAs to be monitored with less invasive approaches [75]. In 2002, the first report on microRNA dysregulation in cancer was published. In chronic lymphocytic leukemia, groups of two microRNAs (miR-16 and miR 15) were discovered [76].
Circular RNAs, which are non-coding RNAs with a closed loop structure, are generated by the splicing of a precursor RNA (pre-mRNA) and covalent binding of 3′ poly(A) tails and 5′capping [77] CircRNAs play a significant role in gene regulation [78][79]. According to Zhu et al. [80], Hsa circ 0013958 was higher in all lung adenocarcinomas, with 20 circRNAs down-regulated and 39 up-regulated. The study reported that Hsa circ 0013958 might be applied as a potent non-invasive marker for the early diagnosis of lung adenocarcinoma. To find Hsa circ 0013958, researchers used real-time PCR to look for its levels in lung adenocarcinoma (LAC). 

4.1.5. Epigenetics as a Cancer Biomarker

Epigenetic alterations are potent biomarkers for cancer as they are frequent for specific genes, are stable, and can be detected in a minimally invasive mode. Numerous studies have discovered that DNA methyltransferases that insert methyl groups into cytosine groups of DNA are changed in cancer cells [81]. The hypermethylation of local CpG island promoter silences the tumor suppressor genes, stimulating their gene mutations. NKX2-6, SPAG6, PER1, and ITIH5 gene methylation was detected in breast cancer patients’ serum [82]. The hypermethylation of promoter p16 in serum DNA, for instance, is linked to recurring colorectal cancer. The methylation of the RASSF1A and p16Ink4 genes has been related to a 15-fold elevation in the comparative risk of lung cancer. The methylation status of multiple genes in clinical specimens might be a viable non-invasive technique for detecting smokers at risk of developing lung cancer [83].

4.2. Protein Biomarkers

Proteins as Cancer Biomarkers

The proteome is a complex system made up of several proteins which interact with one another in dynamic intermolecular interactions and posttranslational alterations. Because they modulate molecular processes and pathways in normal and cancerous cells, proteomic markers are relevant to tumorigenesis and progression [84][85]. Proteins from pancreatic cancer can be found in a number of bodily fluids, including bile, pancreatic juice, urine, and fluid from pancreatic cysts, as shown in Figure 4. These proteins have a great deal of potential as useful biomarkers with a range of therapeutic applications, including early identification, illness staging, treatment prognosis, and in-flight patient monitoring. The majority of the FDA-approved cancer biomarkers in clinical usage are single proteins obtained from serum. HCG, AFP, and LDH are utilized to stage testicular cancer.
Figure 4. Identification of possible protein biomarkers for pancreatic cancer using bodily fluids. Bodily fluids that include cancer-derived proteins include bile, blood, pancreatic juice, urine, and pancreatic cyst fluid. For the management of pancreatic cancer patients, these proteins have a high potential as tumor biomarkers and a variety of clinical applications, including screening in high-risk populations for pancreatic cancer, early diagnosis, disease staging, the evaluation of tumor resection and prognosis, the prediction of therapy response to inform treatment decisions, and real-time patient monitoring [86].
The biomarkers CD171, CD151, and tetraspanin 8 were the most significant indicators between lung cancer patients of all subgroups and healthy individuals [87]. Recent research reveals novel plasma biomarker proteins that may aid in the early diagnosis of bladder cancer. The amount of haptoglobin was found to be significantly higher in patients with low-grade bladder cancer, suggesting that this protein may have a role in the initial stages of bladder tumorigenesis. With reasonable specificity and sensitivity (AUC > 0.87), haptoglobin could differentiate between patients with low-grade bladder cancer and controls [88]
Overexpressed or mutated proteins: Cancer biomarkers include mutated or overexpressed proteins with varying concentration levels depending on cancer type, stage, and individual characteristics. Common examples are HER2 in breast and gastric cancers, EGFR in lung, colorectal, and head and neck cancers, KRAS in colorectal, pancreatic, and lung adenocarcinoma, BRAF in melanoma and colorectal cancer, ALK in some NSCLC cases, and PSA as a prostate cancer biomarker. Detection methods such as IHC, FISH, PCR, and NGS are utilized for assessment. These biomarkers play a crucial role in cancer diagnosis, classification, and treatment decision making.
Signaling pathways and protein interactions: Signaling pathways and protein interactions play a critical role in cancer development and progression. The dystregulation of these pathways and interactions can lead to uncontrolled cell growth, invasion, and metastasis. Several key signaling pathways have been implicated in cancer, including the PI3K/AKT/mTOR pathway, Wnt/β-catenin pathway, Ras/Raf/MEK/ERK pathway, Notch signaling pathway, and TGF-β signaling pathway. The activation of the PI3K/AKT/mTOR pathway promotes cell survival, proliferation, and resistance to apoptosis. The Wnt/β-catenin pathway, when aberrantly activated, leads to altered gene expression, promoting cell proliferation and tumor progression. Mutations in Ras genes and dysregulation of downstream components in the Ras/Raf/MEK/ERK pathway commonly occur in cancers, resulting in uncontrolled cell growth, survival, and metastasis. The dysregulation of the Notch signaling pathway can drive tumor cell proliferation, survival, and angiogenesis. The TGF-β signaling pathway, with its diverse roles in normal development and cancer, when dysregulated, contributes to cancer progression, including increased cell proliferation, epithelial-to-mesenchymal transition (EMT), and immune evasion.

4.3. Metabolic Biomarkers

4.3.1. Metabolites and Metabolic Pathways

Metabolites and metabolic pathways are essential in cancer cells as they undergo alterations to support their growth and survival [89]. Metabolic biomarkers derived from these pathways and metabolites can provide valuable information about cancer metabolism and aid in diagnosis, prognosis, and treatment. Here are some examples of metabolites and metabolic pathways used as metabolic biomarkers in cancer:
Glycolysis: Increased glucose consumption and aerobic glycolysis (the Warburg effect) are characteristic metabolic changes in cancer cells. Biomarkers associated with glycolysis include the following: (1) Lactate: elevated lactate levels in tumor tissues or serum indicate increased glycolytic activity. (2) Glucose transporters (e.g., GLUT1): the overexpression of glucose transporters facilitates glucose uptake in cancer cells [90].
TCA Cycle (Citric Acid Cycle): The tricarboxylic acid (TCA) cycle plays a vital role in energy production and biosynthesis [91]. The dysregulation of the TCA cycle intermediates can serve as metabolic biomarkers: (1) Fumarate and succinate: the accumulation of fumarate and succinate is associated with specific genetic mutations, such as in fumarate hydratase (FH) and succinate dehydrogenase (SDH), respectively. (2) α-Ketoglutarate: altered α-ketoglutarate levels are observed in certain cancer types, such as renal cell carcinoma [92].
Lipid Metabolism: Altered lipid metabolism is common in cancer cells, and several metabolites and pathways are associated with lipid metabolism biomarkers: (1) Choline: increased choline levels, measured using magnetic resonance spectroscopy (MRS), are found in several cancers, including breast and prostate cancers. (2) Fatty acid synthase (FASN): the overexpression of FASN, an enzyme involved in fatty acid synthesis, is observed in various cancers [93][94].
Amino Acid Metabolism: Cancer cells exhibit altered amino acid metabolism, resulting in the production and consumption of specific metabolites: (1) Glutamine: increased glutamine uptake and utilization are common in cancer cells. Glutamine metabolism is associated with pathways such as the TCA cycle and nucleotide synthesis. (2) Serine and glycine: dysregulated serine and glycine metabolism is observed in several cancers, including breast and colorectal cancers [95].
Nucleotide Metabolism: Rapidly dividing cancer cells require nucleotides for DNA and RNA synthesis. Biomarkers related to nucleotide metabolism include deoxythymidine (dThd). Elevated levels of dThd have been associated with certain cancer types and can be detected in urine or plasma [96].

4.3.2. Metabolic Imaging Techniques

Metabolic imaging techniques are used to visualize and assess the metabolic activity of cancer cells. These techniques provide valuable information about tumor metabolism and can aid in cancer diagnosis, staging, treatment planning, and monitoring. Here are some commonly used metabolic imaging techniques in cancer:
Positron Emission Tomography (PET): PET imaging utilizes radiolabeled tracers that are taken up by cells based on their metabolic activity. The most commonly used tracer in PET imaging is fluorodeoxyglucose (FDG), a glucose analog. FDG-PET measures glucose metabolism and is particularly useful in detecting and staging various cancers, including lung, colorectal, and breast cancers [97].
Magnetic Resonance Spectroscopy (MRS): MRS allows the non-invasive assessment of metabolite concentrations in tissues. It provides information on metabolites such as choline, creatine, and lactate, which are associated with cellular metabolism. MRS is used in brain tumor imaging to assess tumor grade, identify tumor margins, and monitor treatment response [98].
Magnetic Resonance Imaging with Hyperpolarized Substrates (HP-MRI): HP-MRI is an emerging technique that utilizes hyperpolarized substrates, such as pyruvate or fumarate, which are metabolized in real time to visualize metabolic pathways. This technique provides dynamic information on metabolic fluxes, such as glycolysis or TCA cycle activity, and holds promise for assessing tumor metabolism and treatment response [99].
Single-Photon Emission Computed Tomography (SPECT): SPECT imaging uses radiotracers that emit gamma rays to detect specific metabolic processes. SPECT can be used to assess various metabolic functions, such as blood flow, metabolism, and receptor binding. Examples include technetium-99m sestamibi for imaging myocardial perfusion and iodine-123 ioflupane for imaging dopamine transporter function in neuroendocrine tumors [100].
Dynamic Contrast-Enhanced Magnetic Resonance Imaging (DCE-MRI): DCE-MRI involves the administration of a contrast agent to evaluate the tumor’s vascularity and blood flow. By measuring the kinetics of contrast agent uptake and washout, DCE-MRI provides information on tumor perfusion, angiogenesis, and vascular permeability. It is used in various cancers, including breast, prostate, and brain tumors [101].
Optical Imaging: Optical imaging techniques, such as fluorescence imaging and bioluminescence imaging, can be used to assess metabolic processes at a cellular level. Fluorescent probes and reporter genes are utilized to visualize specific metabolic activities, such as pH, reactive oxygen species, or enzyme activity. Optical imaging is commonly employed in preclinical research and experimental studies. These metabolic imaging techniques offer complementary information about tumor metabolism and aid in understanding the biological characteristics of cancer cells.

4.3.3. Molecular Probes and Contrast Agents

Molecular probes and contrast agents are invaluable tools in cancer research and clinical imaging. They are designed to specifically target and highlight certain molecular features or physiological processes associated with cancer. Here are some examples of molecular probes and contrast agents used in cancer:
Fluorescent Probes: Fluorescent probes emit light at specific wavelengths when excited by the light of a different wavelength. They can be conjugated to antibodies or other targeting molecules to visualize specific cancer-related targets or processes. For example, fluorescently labeled antibodies can be used to target and detect specific proteins or receptors overexpressed in cancer cells [102].
Magnetic Resonance Imaging (MRI) Contrast Agents: MRI contrast agents enhance the contrast between normal and cancerous tissues in MRI scans. These agents often contain gadolinium, manganese, or iron oxide nanoparticles. They can help visualize tumor morphology, angiogenesis, and tissue perfusion. Examples include gadolinium-based contrast agents and superparamagnetic iron oxide nanoparticles (SPIONs) [103].
Positron Emission Tomography (PET) Tracers: PET tracers are radiolabeled molecules that are administered to patients and emit positrons, which can be detected by PET scanners. They are designed to target specific molecular pathways or processes associated with cancer. For example, fluorodeoxyglucose (FDG) is a radiolabeled glucose analog used to detect increased glucose metabolism in cancer cells, and 18F-fluorothymidine (FLT) is used to assess cell proliferation by targeting DNA synthesis [104].
Ultrasound Contrast Agents: Ultrasound contrast agents are microbubbles filled with gas that enhance the contrast during ultrasound imaging. These agents can help visualize blood flow, angiogenesis, and tumor vascularity. Microbubbles can be conjugated with targeting ligands to selectively bind to specific markers on cancer cells or blood vessels [105].
Near-Infrared (NIR) Imaging Probes: NIR imaging probes emit light in the near-infrared spectrum, which can penetrate deeper into tissues. They are used for the non-invasive imaging of tumors, lymph nodes, and other structures. NIR probes can target specific cancer markers or processes, allowing for real-time imaging during surgery or molecular imaging studies [106].

4.4. Cells as Cancer Biomarkers

4.4.1. Circulating Tumor Cells as Cancer Biomarkers

In the realm of cancer, circulating tumor cells (CTCs) are basic yet effective biomarkers. The existence of CTCs has been demonstrated to determine patient survival with invasive breast cancer at various periods during treatment [107]. Cancer treatment targets (CTTs) are better predictors of prognosis than traditional tumor markers (e.g., CA27-29). The prevalence of therapeutic targets on CTCs can also influence the choice of an effective treatment regime, and the impact of treatment can be assessed after the initial cycle of medication [108]. The prevalence of CTCs has been reported to predict patient survival with metastatic breast cancer at various periods throughout treatment [107]. For patients undergoing systemic therapy for metastatic breast cancer, CTC gives an early and accurate indication of the progression of the disease and survival. CTC counts have been confirmed to be a consistent indicator for prognosis and therapy response in patients with metastatic prostate cancer.

4.4.2. Immune Cells as Cancer Biomarkers

The immune system can differentiate between self-antigen and foreign antigens, promoting the maintenance of immune tolerance and inducing defensive immunity towards foreign antigens. Across several tumor entities, such as colorectal cancer and liver metastases, immune cell count in scanned tissue has already been employed to identify reliable and clinically useful biomarkers [109][110][111]. Macrophages and T lymphocytes are the tumor site’s most prevalent immune cells linked to clinical effects [112][113][114][115]. The histopathological examination of tumor-infiltrating lymphoid cells has been confirmed to be a credible and prognostically useful biomarker [116][117]. T cells aid in thwarting immune pathologies by sustaining self-tolerance [118][119]. Studies reported that upregulated regulatory T-cells (T-regs) expression had been linked to poor immunological responses to tumor antigens in cancer patients, indicating that it may promote immune dysregulation and tumor progression [120][121]. T-regs have already been detected in large numbers in patients with lung, breast, pancreatic, skin, and liver cancers, either in the bloodstream or in the tumor [120][122]. The prevalence of T-regs, which impair tumor-specific T-cell immunity, was negatively related to survival in ovarian cancer patients [123]. T-regs are essential for the emergence of metastasis to lungs in breast cancer, according to Olkhanud et al. [124]. The infiltration of T-regs in primary tumor sites has also been correlated with the prevalence of circulating tumor cell cells in breast cancer patients, implying involvement in cancer cell dissemination [125].

4.4.3. Cancer Stem Cells as Cancer Biomarkers

Within tumors, subpopulations of cancerous cells have long been identified that imitate the hierarchical developmental system of the healthy tissue from which cancer arises. The tumors are propelled and sustained by a small population of cells that can self-renew and produce the more differentiated cells that constitute the mass of the tumor [126]. Various researchers have termed the former subpopulation cancer stem cells (CSCs) to signify that exclusively these cells can produce new tumors when transplanted to animals with immune deficiency [127]. The cancer stem cell model has received a lot of attention recently. CSCs were first detected via research on acute myelogenous leukemia patients (AML). Numerous solid cancers, notably prostate cancer, glioblastoma, breast cancer, medulloblastoma, and melanoma, have been shown to contain CSCs [128]. Because CSC (cancer stem cell) destruction is expected to be a crucial factor in achieving cure, their prevalence has enormous consequences on both cancer biology and treatment. Self-renewal, tumor-originating capacity, asymmetric cell division, and differentiation capacity are all features that identify potential CSCs [129][130]. CD24, CD133, CD166 (ALCAM), CD44, EpCAM, CD29, Lgr5, ALDH1B1, and ALDH1A1 are some of the cytoplasmic and surface markers which have been utilized to detect putative cancer CSCs. Metastatic colon malignancies from patient populations were associated with an elevated expression of ALDH1B1 (p = 0.001) compared with healthy colon tissue [131]. Other investigations have correlated the degree of CD24 expression in colorectal tumors to lymphovascular invasion and decreased survival rates [132][133][134]. The expression of CD44v9 is associated with initial stage lung adenocarcinoma and epidermal growth factor receptor mutations in lung malignancies [135]. CD44 variants are also found in gastric malignancies, where they stimulate tumor initiation [136]. Thus, a CSC biomarker has been suggested as a marker for diagnosis, interventional, and prognostic purposes.

4.5. Lamins as Cancer Biomarkers

The nuclei of animal cells are identifiable by their well-defined chromatin compartmentalization and nuclear structure. In higher vertebrates, the intricate nuclear architecture has been associated with the surge in genomic intricacy and the demand for spatiotemporal control of gene expression. The nucleoplasm, nuclear pore complex, and lamina are the three main constituents of a standard multicellular nucleus. The lamina is a protein meshwork located on the inner nuclear membrane’s nucleoplasmic side. The main element of this lamina is a group of class V intermediate filaments proteins termed lamins which are abnormally expressed in tumors. Lamins control differentiation, apoptosis, gene expression, and DNA repair in a direct or indirect way. By analyzing abnormalities in the expression profile of lamins in different forms of malignancies, several researchers and cancer biologists were able to pinpoint the link between abnormal lamin expression and cancer subtype. The medication betulinic acid has anti-cancer properties in pancreatic cancer by limiting lamin B1 production, and it might be used as a biomarker for cancer.
Scientists have looked into alterations in lamin patterns of expression in a variety of malignancy types in order to better understand the association between lamin transcription and cancer subgroups. Lamins, especially A-type lamins, communicate with transcription elements to control the growth and differentiation of cells [137]. In mature stem cells, the overexpression of the lamin A mutant inhibits the maturation and repair of tissue. The proliferation of cells is linked with decreased differentiation and zero or impaired gene expression for A-type lamins [138][139]. Lamins may function as indicators for cancer risk, forecasting the course and outcome of tumor growth. Nuclear lobulations and morphological alterations may result from lamin A depletion [140]. Colorectal malignancy, which has aberrant or misinterpreted lamin expression, is among the three most common malignancies worldwide. There is a strong correlation amongst lamin A/C expression, prognosis for patients, and the advancement of colorectal cancer, according to recent research. Death rates were almost twice as high in patients whose tumors tested positive for A-type lamin overexpression. Lamin A/C expression may serve as a risk signal for colorectal cancer-dependent mortality since it elevated T-plastin, reduced E-cadherin, and enhanced cell migration in colorectal cancer cells when GFP-lamin A was expressed ectopically. 

4.6. Galectins as Cancer Biomarkers

Galectins are a class of beta-galactoside-binding lectins widely found in all species. The genesis, progression, and pathological aggressiveness of tumors are linked to aberrant tumor-associated galectin expression. Rather than being a carcinoma diagnostic biomarker, galectin-3 is more of a malignancy function-related biomarker that can be applied in conjunction with certain other metabolic biomarkers. It is released into the tumor stroma and promotes tumor growth and angiogenesis [141]. Galectin-3 protein expression was much higher in breast tumor tissues relative to precancerous tissue, and triple-negative breast tumors have significantly higher levels of galectin-3 expression than other subtypes of breast cancer [142][143].
Evidence from a variety of cancer types suggests that the expression of galectin-1 is frequently higher in tumor tissues in contrast with healthy or benign tissues. Malignancies of the reproductive organs, gastrointestinal tract, lymphatic malignancies, myeloproliferative tumors, respiratory and urinary system, thyroid, and skin tumors all exhibit this pattern [144][145][146][147][148][149][150][151][152][153][154][155]. Although three studies found that galectin-1 expression was decreased in head and neck squamous cell carcinoma, cancers of the uterus, and prostate cancer, these results do not agree with those of the majority of studies, which may indicate that patient demographics, tumor subtypes, or methodologies may differ [156][157][158].
The expression of galectin-7 varies between cancer types; it is expressed less in malignancies of the skin, cervix, and stomach and more in cancers of the gastrointestinal tract, breast, thyroid, larynx, and indolent lymphoproliferative diseases. The expression of galectin-7 is also dependent on the subtype of cancer and the location of the disease inside the cell; it is absent in carcinomas of basal cells and present in squamous cell tumors, which are head and neck malignancies [159][160][161][162][163].
Malignant tissues release circulating galectins, which can be utilized as a biomarker for diagnosis. There have been reports of elevated amounts of galectin-1 and -3 in thyroid, pulmonary, skin, bladder, colon, and breast cancers. However, they are not very useful in diagnosing thyroid cancer. Glycoproteins that bind to lectin may potentially function as diagnostic markers [164][165][166][167][168].

4.7. Carbohydrate Antigens as Cancer Biomarkers

Carbohydrate antigen (CA) biomarkers are cancer indicators that have been identified because of efforts to construct antibodies targeting extracts or cell lines derived from tumors. CA indicators are glycoproteins of high molecular weight. The most invariably utilized serum tumor biomarker for detecting malignancies of the digestive organs is CA19-9. The validated marker for detecting ovarian cancer recurrence and evaluating therapy response is CA-125 [169]. CA-125’s diagnosis sensitivity is limited, and it has been demonstrated that this glycoprotein is widely dispersed on the surface of cells in a variety of malignant or benign conditions other than ovarian cancer, leaving its efficacy in the diagnosis in jeopardy [170]. Carcinoembryonic antigen (CEA) is a glycoprotein found on the surface of cells that offers an important function in adhesion. CEA is produced by healthy mucosal cells, and its level in normal adults is as minimal as 2.5 ng/mL and as high as 5.0 ng/mL in people who smoke; but, in the existence of a tumor, it can reach 100 ng/mL.

4.8. Viruses as Cancer Biomarkers

Hepatocellular carcinoma (HCC) is among the most widespread viral-induced tumors [171]. Over 80% of HCC cases are reported in underdeveloped nations. The risk factors are chronic hepatitis viral infections, caused primarily by the prevalent hepatitis B virus (HBV), and hepatitis C virus (HCV) infection in a small percentage of HCC patients (12–17%) [171]. HBV can induce tumorigenesis by genomic instability mediated by its frequent incorporation in host DNA [172]. Cervical is the second most prevalent cancer in women, accounting for most cancer-related fatalities worldwide, and chronic infection with particular strains of HPV is the most prevalent trigger for cervical cancer. HPV has been detected in a substantial amount in anal, oral, penile, esophageal, vulvar, and vaginal cancers, as well as a tiny portion in laryngeal, lung, and stomach cancers in some regions of the world [173]. Cervical carcinoma samples were utilized to diagnose, clone, and sequence papillomaviruses for the first time. Antibodies to HPV (E6 and E7) produced by participants act as biomarkers of an HPV-related carcinoma [174]. Due to the sheer rise in HPV-related disease, especially HPV16 infection, oropharyngeal squamous cell carcinoma (OPSCC) is presumed to be the third most prevalent malignancy in middle-aged, non-Hispanic, white men by 2045.

4.9. Exosomes as a Cancer Biomarker

Exosomes, which are the smallest (diameter of 30–150 nm) extracellular vesicles, are secreted by endothelial cells, erythrocytes, epithelial cells, dendritic cells, oligodendroglial cells, mesenchymal stem cells (MSCs), neural cells, and tumor cells [175][176]. Exosomes can serve as “cellular postmen” for carrying genomic material for inter- and intracellular communication because they are loaded with physiologically active components such as RNA, cytoplasmic proteins, cellular metabolites, and lipids [177]. Exosomes can be found in blood, breast milk, synovial fluid, amniotic fluid, urine, bronchoalveolar lavage fluid, pleural fluid, serum, and saliva [178][179]. Due to their widespread prevalence in physiological fluids and their resemblance to the contents of original cells, exosomes are potentially useful as circulating biomarkers for numerous kinds of cancers. By constructing or modulating the tumor microenvironment and encouraging angiogenesis and tumor invasion, tumor-derived exosomes (TEXs) serve a crucial role in tumorigenesis and progression [180][181]. TEXs contain a multitude of endogenous cargos which partly imitate the components and resemble the pathophysiological condition or signaling abnormalities of parent cells, rendering them potential biomarkers for early cancer detection. Exosomal proteins are emerging diagnosis and monitoring markers for cancers because there are plentiful cancer-related proteins in exosomes. In exosomes secreted from pancreatic cancer, overexpressed proteoglycan Glypican-1 (GPC-1) is found. Patients with pancreatic ductal adenocarcinoma (PDAC) were reported as having higher levels of exosomal protein 4 (CKAP 4) than healthy people. Exosomes containing CKAP 4 in the serum can be utilized as a potential biomarker for PDAC [182]. Trp5 (Transient Receptor Potential Channel 5) is overexpressed in exosomes from breast cancer, has a major function in drug resistance, and can be utilized to anticipate chemotherapy resistance in patients with breast cancer [183]. Exosomes have a double-layer lipid barrier that protects internal nucleic acids from being damaged. Consequently, exosomal nucleic acids can be potential indicators in cancer diagnostics. Hepatocellular carcinoma and other malignancies may benefit from exosomal miRNAs as potential serological markers [184]. Elevated exosomal miR-375 and miR-1290 levels in the plasma of prostate cancer (castration-resistant) patients were linked to a poor overall survival rate (OS) [185].

4.10. Lipids as Cancer Biomarkers

Jiang and colleagues reported the lipid species that could be utilized as markers for early detection of breast cancer. In comparison to healthy controls, researchers noticed higher amounts of Phytosterol Diosgenin (DG), and Phosphatidylcholines (PC) in breast cancer samples. The level of Phosphatidylethanolamine (PE) was shown to be lower in breast cancer samples [27]. Prostate cancer patients have a 2.7-fold elevation in Lysophosphatidylcholine (LPC) relative to healthy subjects, according to Zhou and colleagues [28].

5. Emerging Technologies and Techniques

5.1. Liquid Biopsy

Liquid biopsy is a minimally invasive diagnostic procedure that involves the examination of numerous elements found in physiological fluids like blood or urine, including exosomes, circulating tumor cells, cell-free DNA (cfDNA), and proteins. With the help of this method, early cancer detection, treatment monitoring, and the discovery of potential therapeutic targets are made possible through insights into a patient’s molecular profile. Figure 5 provides an illustration of the methods used in liquid biopsy analysis. In this method, a single blood sample’s cfDNA/ctDNA profile is made up of both wild-type and genetically and epigenetically changed DNA fragments released by various tissues and organs through various pathways [186].
Figure 5. Liquid biopsy analysis [186]. (A) Liquid biopsy analysis involves the examination of circulating cancer cells, circulating tumor DNA (ctDNA), and extracellular vesicles containing proteins, RNA, ctDNA, and cell-free DNA (cfDNA) from both primary and secondary tumor sites. This approach is considered a potential cancer biomarker, enabling the quantification of ctDNA levels and the detection of (epi)genetic alterations. (B) Methods employed for ctDNA analysis encompass real-time PCR, BEAMing (beads, emulsion, amplification, and magnetics), coamplification at lower denaturation temperature PCR (COLD-PCR), digital PCR, and next-generation sequencing.

5.2. Single-Cell Analysis

Single-cell analysis has revolutionized our understanding of tumor heterogeneity by enabling the characterization of individual cells within a tumor. Here is how single-cell analysis helps to characterize tumor heterogeneity:
Identifying Subpopulations: Single-cell analysis allows the identification of distinct subpopulations of cells within a tumor. By analyzing the transcriptomic or genomic profiles of individual cells, researchers can identify and classify different cell types or states within the tumor. This reveals the heterogeneity in gene expression patterns, signaling pathways, and functional characteristics among tumor cells.
Uncovering Clonal Diversity: Tumors are composed of clonal cell populations with genetic alterations acquired during tumor evolution. Single-cell genomic sequencing techniques, such as single-nucleus sequencing or single-cell whole-genome sequencing, can identify and characterize somatic mutations, copy number variations, and chromosomal rearrangements in individual cells. This helps to reveal clonal diversity and understand the evolutionary trajectory of the tumor.
Profiling Transcriptomic Variability: Single-cell RNA sequencing (scRNA-seq) enables the profiling of gene expression patterns in individual cells. This allows the identification of different transcriptional states, gene regulatory networks, and functional states within the tumor. By analyzing the transcriptomic variability, researchers gain insights into the cellular heterogeneity, cell lineage relationships, and potential cell subpopulations with distinct biological properties.
Assessing Protein Expression and Signaling: Techniques such as immunohistochemistry (IHC) and mass cytometry (CyTOF) at the single-cell level enable the characterization of protein expression profiles and signaling pathways in individual cells. This helps to understand the heterogeneity in protein expression, cellular phenotypes, and the activation of key signaling molecules within the tumor microenvironment.
Mapping Spatial Heterogeneity: Spatial transcriptomics and imaging-based single-cell analysis techniques allow the assessment of cellular heterogeneity in the context of the tumor microenvironment. By characterizing the spatial distribution of different cell types, gene expression patterns, or immune cell infiltrates, researchers can unravel the spatial organization and heterogeneity of tumor cells within the tissue architecture. By combining these single-cell analysis approaches, researchers can comprehensively characterize the complexity and heterogeneity of tumors at the cellular level. This deeper understanding of tumor heterogeneity has implications for predicting treatment response, identifying therapy-resistant cell populations, and developing personalized treatment strategies in cancer patients.

5.3. Artificial Intelligence and Machine Learning

Artificial intelligence (AI) and machine learning (ML) techniques have made significant contributions to various aspects of cancer research, diagnosis, treatment, and patient care. Here are some key ways AI and ML are used in cancer:
Image Analysis and Medical Imaging: AI and ML algorithms are used to analyze medical images, such as mammograms, CT scans, and histopathology slides. These algorithms can assist in early cancer detection, tumor segmentation, identifying suspicious lesions, and predicting treatment response. Deep learning models have demonstrated remarkable accuracy in image-based cancer diagnosis.
Genomic Analysis: AI and ML techniques are applied to genomic data analysis, including DNA sequencing and gene expression profiling. These algorithms can identify genomic alterations, mutations, and biomarkers associated with specific cancer types, helping in diagnosis, prognosis, and personalized treatment selection.
Clinical Decision Support: AI and ML models can aid clinicians in making more informed decisions regarding cancer treatment plans. These models leverage patient data, such as medical records, imaging results, and genetic profiles, to provide personalized treatment recommendations, predict treatment outcomes, and optimize treatment strategies.
Drug Discovery and Development: AI and ML are utilized in the early stages of drug discovery to identify potential drug targets, predict drug interactions, and design novel compounds. These techniques can also assist in drug repurposing by analyzing large-scale datasets and identifying existing drugs that may be effective against specific cancer types.
Precision Medicine: AI and ML algorithms enable precision medicine approaches by integrating patient-specific data, including clinical, genomic, and imaging information. These models help identify patient subgroups that are more likely to respond to specific treatments, thus guiding personalized treatment selection and improving patient outcomes.
Data Integration and Knowledge Extraction: AI and ML techniques can integrate and analyze large-scale, heterogeneous datasets from various sources, including electronic health records, medical literature, and public databases. By extracting knowledge and patterns from these data, AI models can identify associations, predict disease outcomes, and generate new insights for cancer research.
Prognosis and Risk Assessment: AI and ML models can predict cancer prognosis, recurrence risk, and patient survival outcomes based on clinical and molecular features. These predictions assist in treatment planning, patient counseling, and monitoring long-term outcomes.

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